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a
describe it here
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1
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0
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lkplkplkp |
Created on server
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a
describe it here
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1
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0
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m.hiroki |
Created on server
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a
describe it here
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1
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0
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mariawahid |
Created on server
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A
describe it here
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1
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0
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haubinz@126.com |
Created on server
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aa
describe it here
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1
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0
|
h-tengfei@hotmail.com |
Created on server
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aalya
describe it here
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1
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0
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acelyaavci |
Created on server
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|
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AddFCSEventIndex
Adds indexes to events in a Flow Cytometry Standard (FCS) data file.
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2
|
Added fix for parsing empty keyword values
|
pcarr@broadinstitute.org |
GenePattern production (new)
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AddFCSParameter
Add parameters and their values to a FCS data file
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2
|
Added fix for parsing empty keyword values
|
pcarr@broadinstitute.org |
GenePattern production (new)
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AddNoiseToFCS
Add noise to specified parameters in an FCS data file.
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2
|
Added fix for parsing empty keyword values
|
pcarr@broadinstitute.org |
GenePattern production (new)
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Affymetrix
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2
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daniallmasood |
Created on server
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1
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daniallmasood |
Created on server
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AffySTExpressionFileCreator
Creates a GCT file from a set of CEL files from Affymetrix ST arrays.
|
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2
|
Updated to use the genepattern/affy-st-expression-file-creator:2 Docker image
|
bhill@broadinstitute.org |
GenePattern production (new)
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|
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0.14
|
Updated to make use of the R package installer.
|
pcarr@broadinstitute.org |
GenePattern beta
|
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|
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alexs_simple_pipeline
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1
|
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atwenzel2 |
Installed from zip
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All.posibel.combinations.pipeline.clustering
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2
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mperez |
Created on server
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1
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mperez |
Created on server
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ALLAML
describe it here
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1
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0
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Andyred419 |
Created on server
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ALM
describe it here
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1
|
0
|
ankstella123@gmail.com |
Created on server
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Amaretto
Discovery of driver genes using epigenomic, genomic and transcriptomic data using module networks with penalized regression.
|
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2
|
Change location of data for the gene.sets.database parameter from ftp://gpftp.broadinstitute.orf to https://datasets.genepattern.org
|
ted |
GenePattern production (new)
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1
|
Change location of data for the gene.sets.database parameter from ftp://gpftp.broadinstitute.orf to https://datasets.genepattern.org
|
ted |
GenePattern production (new)
|
|
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0.53
|
Initial Revision
|
ted |
Installed from zip
|
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0.46
|
Working revision from Gevaert lab git repo on 10/16/18
|
ted |
Installed from zip
|
|
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0.42
|
Working revision from Gevaert lab git repo on 10/16/18
|
ted |
Installed from zip
|
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|
|
AmpliconSuite
A multithread-enabled quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. PrepareAA supports hg19 (or GRCh37), hg38 as well as mouse genome mm10 (or GRCm38). PrepareAA can also be invoked to start at intermediate stages of the data preparation process.
<br>
All credits go to: https://github.com/jluebeck/PrepareAA
<br>
View licenses here: <a href="https://github.com/genepattern/AmpliconSuite#licenses">https://github.com/genepattern/AmpliconSuite#licenses</a>
<br/>
<p>
To increase your GenePattern disk space quote so you can more easily upload the input bam files, <b><a href="https://forms.gle/23tkh98vwkhtCeKM7">click here to join the AmpliconSuiteUsers group on this server.</b> </a> </p>
To run multiple samples at once, simply drag and drop multiple samples into the input options. There is no need to check the "Batch" box.
<br>
Currently using Amplicon Architect version 1.3.4.
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41
|
updated parameters & dockerfile
|
edwin5588 |
GenePattern production (new)
|
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|
40
|
updated parameters & dockerfile
|
edwin5588 |
GenePattern production (new)
|
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39
|
updated parameters & dockerfile
|
edwin5588 |
GenePattern production (new)
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38
|
updated parameters & dockerfile
|
edwin5588 |
GenePattern production (new)
|
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37
|
updated parameters & dockerfile
|
edwin5588 |
GenePattern production (new)
|
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35
|
updated parameters & dockerfile
|
edwin5588 |
GenePattern production (new)
|
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|
34
|
new ECDNA tag
|
edwin5588 |
GenePattern production (new)
|
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|
33
|
New docker image for environment, updates to documentation for running Batch mode, updates to parameter description.
|
edwin5588 |
GenePattern production (new)
|
|
|
31
|
New Docker image, with new arguments.
|
edwin5588 |
GenePattern production (new)
|
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|
28
|
New Docker image, with new arguments.
|
ted |
GenePattern production (new)
|
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|
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AmpliconSuiteAggregator
Aggregates individual AmpliconSuite runs. Takes in zip files (or .tar.gz) and aggregates the results. Results can directly be used to load onto AmpliconRepository.
|
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11
|
added license acceptance & new ecdna tag
|
edwin5588 |
GenePattern production (new)
|
|
|
10
|
added license acceptance & new ecdna tag
|
edwin5588 |
GenePattern production (new)
|
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|
7
|
New post method for Aggregator and API.
|
edwin5588 |
GenePattern production (new)
|
|
|
6
|
New post method for Aggregator and API.
|
edwin5588 |
GenePattern production (new)
|
|
|
5
|
New post method for Aggregator and API.
|
edwin5588 |
GenePattern production (new)
|
|
|
4
|
New docker, new arguments, new features for aggregator
|
edwin5588 |
GenePattern production (new)
|
|
|
3
|
Added new parameter for AmpRepo support, Amp classifier support
|
ted |
GenePattern production (new)
|
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|
|
analisiDatiRNAseq
|
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1
|
|
isaia |
Created on server
|
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|
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Analysis.of.Affymetrix.Microarray.Data
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2
|
|
ps1277 |
Created on server
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1
|
|
ps1277 |
Created on server
|
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|
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Analyzing.microarray.data.CEL.and..clm
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3
|
|
Chris96 |
Created on server
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2
|
|
Chris96 |
Created on server
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1
|
|
Chris96 |
Created on server
|
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|
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Anlise.CEL
describe it here
|
|
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1
|
0
|
iael.minu |
Created on server
|
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|
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ARACNE
Runs the ARACNE algorithm for reverse engineering cellular networks
|
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|
2
|
fix problem with processing transcription factor list parameter
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
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|
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AreaChange
Calculates fraction of area under the spectrum that is attributable to signal (area after noise removal / original area)
|
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2
|
Updated for R 2.5.0
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
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|
|
ArrayAnalysis_1.0
describe it here
|
|
|
1
|
0
|
jason.a.horton |
Created on server
|
|
|
|
asdf
describe it here
|
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1
|
0
|
ted |
Created on server
|
|
|
|
aSf
describe it here
|
|
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1
|
0
|
babakke |
Created on server
|
|
|
|
AuDIT
Automated Detection of Inaccurate and Imprecise Transitions in MRM Mass Spectrometry
|
|
|
9
|
Dockerized for cloud
|
ted |
GenePattern production (new)
|
|
|
8
|
Dockerized for cloud
|
ted |
GenePattern production (new)
|
|
|
|
bat
describe it here
|
|
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1
|
0
|
ayende1 |
Created on server
|
|
|
|
batch.effect
describe it here
|
|
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1
|
0
|
jayakumarvn |
Created on server
|
|
|
|
bb
|
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1
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|
marygold |
Created on server
|
|
|
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BedToGtf
Converts BED files to GFF or GTF format
|
|
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1
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
Beroukhim.Getz.2007.PNAS.Glioma.GISTIC
|
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2
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
Beroukhim.Getz.2007.PNAS.Glioma.GISTIC2.0
|
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4
|
|
edwin5588 |
Created on server
|
|
|
3
|
|
edwin5588 |
Created on server
|
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2
|
|
edwin5588 |
Created on server
|
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1
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|
edwin5588 |
Created on server
|
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|
|
Bhagwat
|
|
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1
|
|
bhagwat.jadhav6001@gmail.com |
Created on server
|
|
|
|
BHIL_TEST_MiniReg
describe it here
|
|
|
2
|
0
|
bhill@broadinstitute.org |
Created on server
|
|
|
1
|
0
|
bhill@broadinstitute.org |
Created on server
|
|
|
|
biobaza.GSEA
|
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4
|
|
kacper_maciejewski |
Created on server
|
|
|
3
|
|
kacper_maciejewski |
Created on server
|
|
|
2
|
|
kacper_maciejewski |
Created on server
|
|
|
1
|
|
kacper_maciejewski |
Created on server
|
|
|
|
Biotech_MUL_ex4
Pipeline for Exercise 4 @ Biotechnology Masters Biostatistics Course
|
|
|
1
|
v.0.1
|
botomj@gmail.com |
Created on server
|
|
|
|
BiotechMUL_ex4_preprocessing
Data preprocessing pipeline for GSE635
|
|
|
1
|
The first working version.
|
jj.chrzanowski1 |
Installed from zip
|
|
|
1
|
The first working version.
|
jedrzej.chrzanowski |
Installed from zip
|
|
|
|
blah
describe it here
|
|
|
1
|
0
|
hb739 |
Created on server
|
|
|
|
BobbiesTESTFilter
|
|
|
1
|
|
bhill@broadinstitute.org |
Installed from zip
|
|
|
|
borr
|
|
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2
|
|
marygold |
Created on server
|
|
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1
|
|
marygold |
Created on server
|
|
|
|
bowtie.alignment
describe it here
|
|
|
7
|
|
csusm |
Created on server
|
|
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6
|
|
csusm |
Created on server
|
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5
|
0
|
csusm |
Created on server
|
|
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4
|
0
|
csusm |
Created on server
|
|
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3
|
0
|
csusm |
Created on server
|
|
|
2
|
0
|
csusm |
Created on server
|
|
|
1
|
0
|
csusm |
Created on server
|
|
|
|
bowtie.alignment
describe it here
|
|
|
4
|
0
|
csusm |
Created on server
|
|
|
3
|
0
|
csusm |
Created on server
|
|
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2
|
0
|
csusm |
Created on server
|
|
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1
|
0
|
csusm |
Created on server
|
|
|
|
bra
describe it here
|
|
|
2
|
0
|
Busra Nur |
Created on server
|
|
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1
|
0
|
Busra Nur |
Created on server
|
|
|
|
bulk.RNAseq
describe it here
|
|
|
1
|
0
|
lclubb |
Created on server
|
|
|
|
BWA.aln
A fast and accurate short-read alignment tool that allows for mismatches and gaps. Alignments are output in a SAM format file, which provides Phred-scale quality scores for each alignment. Uses BWA 0.7.4 aln and samse/sampe.
|
|
|
2.1
|
Updated BWA.Index drop down menu to new BWA module support files location at datasets.genepattern.org (Amazon S3). and specify docker image, to production
|
edwin5588 |
GenePattern dev
|
|
|
1.20
|
Updated BWA.Index drop down menu to new BWA module support files location at datasets.genepattern.org (Amazon S3). and specify docker image
|
edwin5588 |
GenePattern dev
|
|
|
1.19
|
Updated to BWA 0.7.4, changed to use dynamic FTP-hosted index files, and switched to HTML-based doc
|
pcarr@broadinstitute.org |
GenePattern beta
|
|
|
1
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
BWA.bwasw
Aligns long sequences (>200 bp) to a sequence database using BWA 0.7.4 bwasw.
|
|
|
1.17
|
Update BWA.index to new index location (datasets.genepattern.org) and update dockerfile, to production
|
edwin5588 |
GenePattern dev
|
|
|
1.16
|
Update BWA.index to new index location (datasets.genepattern.org) and update dockerfile
|
edwin5588 |
GenePattern dev
|
|
|
1.14
|
Updated to BWA 0.7.4, changed to use dynamic FTP-hosted index files, and switched to HTML-based doc
|
pcarr@broadinstitute.org |
GenePattern beta
|
|
|
1
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
BWA.indexer
Creates a BWT index from a sequence FASTA file
|
|
|
1
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
1.10
|
updated dockerfile and commandline to run script at dockerfile location, to production
|
edwin5588 |
GenePattern dev
|
|
|
1.9
|
updated dockerfile and commandline to run script at dockerfile location
|
edwin5588 |
GenePattern dev
|
|
|
1.8
|
Updated to BWA 0.7.4 and switched to HTML-based doc
|
pcarr@broadinstitute.org |
GenePattern beta
|
|
|
|
CART
Classification and Regression Tree
|
|
|
2
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
CARTXValidation
Classification and Regression Tree X-Validation
|
|
|
2
|
Updated for R 2.5.0
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
2.2
|
Added html doc and outputs classification results for each iteration
|
pcarr@broadinstitute.org |
GenePattern beta
|
|
|
|
CCA_paired.T.test
|
|
|
8
|
|
cho |
Created on server
|
|
|
7
|
|
cho |
Created on server
|
|
|
6
|
|
cho |
Created on server
|
|
|
5
|
|
cho |
Created on server
|
|
|
4
|
|
cho |
Created on server
|
|
|
3
|
|
cho |
Created on server
|
|
|
2
|
|
cho |
Created on server
|
|
|
1
|
|
cho |
Created on server
|
|
|
|
CCLE.geneset
describe it here
|
|
|
1
|
0
|
gopalp |
Created on server
|
|
|
|
cd8
describe it here
|
|
|
1
|
0
|
AlessioRicci |
Created on server
|
|
|
|
CellFie
CellFie: Cellular Functions InferencE - An alternative approach to capture the breadth of cellular functions by performing a functional analysis of existing biological networks. Please refer to the documentation for details about the procedure.
|
|
|
5
|
update to reaction models
|
bhill@broadinstitute.org |
GenePattern production (new)
|
|
|
|
check.disk.size
just does a df -sh .
|
|
|
3
|
|
ted |
Created on server
|
|
|
2
|
|
ted |
Created on server
|
|
|
1
|
|
ted |
Created on server
|
|
|
|
chr20
describe it here
|
|
|
1
|
0
|
SGY |
Created on server
|
|
|
|
chris.pipeline
describe it here
|
|
|
1
|
0
|
yesimtutuncu |
Created on server
|
|
|
|
Ciao
|
|
|
4
|
|
mauro campanella |
Created on server
|
|
|
3
|
|
mauro campanella |
Created on server
|
|
|
2
|
|
mauro campanella |
Created on server
|
|
|
1
|
|
mauro campanella |
Created on server
|
|
|
|
ClassNeighbors
Select genes that most closely resemble a profile
|
|
|
1
|
Added email address to owner contact
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
cloud_miniregression_pipeline
Test pipeline
|
|
|
1
|
initial one
|
edjuaro |
Created on server
|
|
|
|
cls.file.generator
|
|
|
2
|
|
guest_96371 |
Created on server
|
|
|
1
|
|
guest_96371 |
Created on server
|
|
|
|
ClsFileCreator
A tool to create a class label (CLS) file.
|
|
|
4
|
JavaScript implementation
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
4.1
|
S3 file fix
|
tabor |
GenePattern production (new)
|
|
|
3.16
|
Fixed bug with parsing gct files with Windows line endings
|
pcarr@broadinstitute.org |
GenePattern beta
|
|
|
|
cluster
describe it here
|
|
|
1
|
0
|
polenkom |
Created on server
|
|
|
|
cluster
describe it here
|
|
|
1
|
0
|
yanwang |
Created on server
|
|
|
|
Cluster.of.cluster
|
|
|
2
|
|
wyatkn |
Created on server
|
|
|
1
|
|
wyatkn |
Created on server
|
|
|
|
Cluster0_ssGSEA
|
|
|
5
|
|
jbaronas |
Created on server
|
|
|
4
|
|
jbaronas |
Created on server
|
|
|
3
|
|
jbaronas |
Created on server
|
|
|
2
|
|
jbaronas |
Created on server
|
|
|
1
|
|
jbaronas |
Created on server
|
|
|
|
Clustered.heat.map
|
|
|
7
|
|
314159 |
Created on server
|
|
|
|
Clutering.hierarchical.pipeline
|
|
|
1
|
|
mperez |
Created on server
|
|
|
|
cms
describe it here
|
|
|
1
|
0
|
cherlynty |
Created on server
|
|
|
|
CN.Analysis
describe it here
|
|
|
1
|
0
|
parsas@mskcc.org |
Created on server
|
|
|
|
CNToXCN
|
|
|
1
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
CNV
describe it here
|
|
|
1
|
0
|
huangzr |
Created on server
|
|
|
|
cnv.analysis
describe it here
|
|
|
2
|
0
|
Washaakh |
Created on server
|
|
|
1
|
0
|
Washaakh |
Created on server
|
|
|
|
CNV.Analysis
describe it here
|
|
|
1
|
0
|
Washaakh |
Created on server
|
|
|
|
CNV1
|
|
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1
|
|
chuting |
Created on server
|
|
|
|
cnv_luad
|
|
|
1
|
|
xiejinye |
Created on server
|
|
|
|
coad
describe it here
|
|
|
1
|
0
|
michaela1688 |
Created on server
|
|
|
|
CoGAPS
Coordinated Gene Activity in Pattern Sets (CoGAPS) implements a Bayesian MCMC matrix factorization algorithm, GAPS, and links it to gene set statistic methods to infer biological process activity. It can be used to perform sparse matrix factorization on any data, and when this data represents biomolecules, to do gene set analysis.
|
|
|
0.93
|
set quality to 'development', set categories='Tutorial'
|
ted |
Installed from zip
|
|
|
0.9
|
set quality to 'development', set categories='Tutorial'
|
ted |
Installed from zip
|
|
|
0.8
|
set quality to 'development', set categories='Tutorial'
|
ted |
Installed from zip
|
|
|
0.6
|
set quality to 'development', set categories='Tutorial'
|
ted |
Installed from zip
|
|
|
0.6.9
|
set quality to 'development', set categories='Tutorial'
|
ted |
Installed from zip
|
|
|
0.5
|
set quality to 'development', set categories='Tutorial'
|
ted |
Installed from zip
|
|
|
0.2
|
set quality to 'development', set categories='Tutorial'
|
ted |
Installed from zip
|
|
|
0.1
|
set quality to 'development', set categories='Tutorial'
|
ted-dev |
Installed from zip
|
|
|
0.1.9
|
set quality to 'development', set categories='Tutorial'
|
ted |
Installed from zip
|
|
|
|
CollapseDataset
Collapses expression values from multiple input ids that map to a single target gene to a single value on a per-sample basis
|
|
|
2.2.0
|
10/03/2022 : Updated to Human MSigDB v2022.1.Hs and Mouse MSigDB 2022.1.Mm.
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
2.1.5
|
09/15/2022 : Updated to Human MSigDB v2022.1.Hs. Direct support for Mouse MSigDB 2022.1.Mm is not yet available
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
2.1.4
|
03/02/2022 : Removed Log4J entirely from the code base. Fixed weighted_p1.5 computation. Added min dataset size warnings.
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
|
CollapseDataset
describe it here
|
|
|
1
|
0
|
monser9610 |
Created on server
|
|
|
|
ComBat
Batch Correction - Not intended for use with single-cell RNA-seq data.
|
|
|
3.6
|
new batch correction tag
|
edwin5588 |
Installed from zip
|
|
|
3.1
|
Setting parameter create.prior.plots to only receive no as an accepted value. Temporary patch.
|
edjuaro |
GenePattern production (new)
|
|
|
|
Combat.Pipeline
|
|
|
11
|
|
kpagacz1 |
Created on server
|
|
|
10
|
|
kpagacz1 |
Created on server
|
|
|
9
|
|
kpagacz1 |
Created on server
|
|
|
8
|
|
kpagacz1 |
Created on server
|
|
|
7
|
|
kpagacz1 |
Created on server
|
|
|
6
|
|
kpagacz1 |
Created on server
|
|
|
5
|
|
kpagacz1 |
Created on server
|
|
|
4
|
|
kpagacz1 |
Created on server
|
|
|
3
|
|
kpagacz1 |
Created on server
|
|
|
2
|
|
kpagacz1 |
Created on server
|
|
|
1
|
|
kpagacz1 |
Created on server
|
|
|
|
ComBat_Seq
ComBat_Seq module. A Batch effect adjustment tool for bulk RNA-seq count data. Improvement upon ComBat, and uses a negative binomial regression to model batch effects. ComBat-seq takes untransformed, raw count matrix as input. Provides adjusted data which preserves the integer nature of counts, so that the adjusted data are compatible with the assumptions of state-of-the-art differential expression software (e.g. edgeR, DESeq2, which request untransformed count data)
Original Documentation: https://github.com/zhangyuqing/ComBat-seq
Credits go to Zhang et al, https://doi.org/10.1093/nargab/lqaa078
|
|
|
6
|
New base docker image (R4.2.2), updates to gct file writing to ensure description and name are at the front.
|
edwin5588 |
GenePattern production (new)
|
|
|
6.1
|
Added batch correction tag
|
edwin5588 |
GenePattern dev
|
|
|
5
|
Added new parameter (users can now select output file format), new docker image to go with it
|
edwin5588 |
GenePattern production (new)
|
|
|
3
|
Update parameters, dockerfile, and script to allow more input options.
|
edwin5588 |
GenePattern production (new)
|
|
|
2
|
Finished module interface, new documentations
|
edwin5588 |
GenePattern production (new)
|
|
|
|
comp
describe it here
|
|
|
1
|
0
|
GPjana |
Created on server
|
|
|
|
Comparative_Marker_Retrieval_and_Analysis
|
|
|
3
|
|
alow |
Created on server
|
|
|
2
|
|
alow |
Created on server
|
|
|
1
|
|
alow |
Created on server
|
|
|
|
ComparativeMarkerSelection
Identify differentially expressed genes that can discriminate between distinct classes of samples.
|
|
|
11
|
Updated to run in its own R 2.5 container - allowing q values to be computed.
|
bhill@broadinstitute.org |
GenePattern production (new)
|
|
|
4
|
Added Paired T-Test
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
ComparativeMarkerSelection_Pipeline
|
|
|
1
|
|
kathyhan98 |
Created on server
|
|
|
|
CompareSpectra
Compares two spectra to determine similarity
|
|
|
3
|
Fixed parsing of input files, changed default value of output file, and suppressed package startup messages
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
Comparison
|
|
|
14
|
|
boucherd |
Created on server
|
|
|
13
|
|
boucherd |
Created on server
|
|
|
12
|
|
boucherd |
Created on server
|
|
|
11
|
|
boucherd |
Created on server
|
|
|
10
|
|
boucherd |
Created on server
|
|
|
9
|
|
boucherd |
Created on server
|
|
|
8
|
|
boucherd |
Created on server
|
|
|
7
|
|
boucherd |
Created on server
|
|
|
6
|
|
boucherd |
Created on server
|
|
|
5
|
|
boucherd |
Created on server
|
|
|
4
|
|
boucherd |
Created on server
|
|
|
3
|
|
boucherd |
Created on server
|
|
|
2
|
|
boucherd |
Created on server
|
|
|
1
|
|
boucherd |
Created on server
|
|
|
|
Comparison.1
describe it here
|
|
|
1
|
0
|
tirsa.vanwestering@ugent.vib.be |
Created on server
|
|
|
|
compmarkersel
ID diff expressed genes
|
|
|
4
|
|
robynm |
Created on server
|
|
|
3
|
|
robynm |
Created on server
|
|
|
2
|
0
|
robynm |
Created on server
|
|
|
1
|
0
|
robynm |
Created on server
|
|
|
|
ConcatenateFilelist
Concatenate all of the items in the input filelist into a single large file.
|
|
|
1
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
ConClu_12112018
|
|
|
1
|
|
lydia.lam |
Created on server
|
|
|
|
ConCluTCGA_12112018
|
|
|
1
|
|
lydia.lam |
Created on server
|
|
|
|
Conos.Cluster
GenePattern Module which implements the clustering and embedding steps of Conos
|
|
|
3
|
Test Docker image v3 - version control for pkgs
|
ted |
GenePattern production (new)
|
|
|
2.2
|
Test Docker image v3 - version control for pkgs
|
edjuaro |
GenePattern dev
|
|
|
0.1
|
Initial version
|
edjuaro |
GenePattern dev
|
|
|
|
Conos.Preprocess
GenePattern Module which implements the preprocessing and PCA steps of Conos
|
|
|
3
|
updated accepted file formats for input file
|
ted |
GenePattern production (new)
|
|
|
2.2
|
Test Docker image v3 - version control for pkgs
|
edjuaro |
GenePattern dev
|
|
|
0.1
|
Initial version
|
edjuaro |
GenePattern dev
|
|
|
|
Conos.VisualizeGeneExpression
This is a minimalistic implementation of visualization options for Conos. This module is intended to be used after <a href="https://cloud.genepattern.org/gp/pages/index.jsf?lsid=urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00410:0.1">Conos.Cluster</a> has been ran.
|
|
|
8
|
Initial version
|
acastanza |
GenePattern production (new)
|
|
|
7
|
Initial version
|
acastanza |
GenePattern production (new)
|
|
|
5
|
Initial version
|
ted |
GenePattern production (new)
|
|
|
|
consensus
describe it here
|
|
|
1
|
0
|
monser9610 |
Created on server
|
|
|
|
consensus.clusterin.kmax.15
describe it here
|
|
|
1
|
0
|
monser9610 |
Created on server
|
|
|
|
ConsensusCluster.12318
|
|
|
5
|
|
eshelden |
Created on server
|
|
|
4
|
|
eshelden |
Created on server
|
|
|
3
|
|
eshelden |
Created on server
|
|
|
3.1
|
|
eshelden |
Created on server
|
|
|
2
|
|
eshelden |
Created on server
|
|
|
1
|
|
eshelden |
Created on server
|
|
|
|
ConsensusCluster_12112018
|
|
|
1
|
|
lydia.lam |
Created on server
|
|
|
|
ConsensusClustering
Resampling-based clustering method
|
|
|
7
|
Fixed bugs in classpath (changed Jama-1.0.1.jar to Jama-1.0.2.jar and acme.jar to Acme.jar)
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
7.2
|
Updated command line to use <run-with-env> wrapper script
|
pcarr@broadinstitute.org |
GenePattern beta
|
|
|
|
ConsensusClusterSKCM
|
|
|
3
|
|
eshelden |
Created on server
|
|
|
2
|
|
eshelden |
Created on server
|
|
|
1
|
|
eshelden |
Created on server
|
|
|
|
ConstellationMap
A downstream visualization and analysis tool for gene set enrichment results with interactive web visualizer.
|
|
|
1.4.20
|
Updated to Human MSigDB v2022.1.Hs and Mouse MSigDB 2022.1.Mm.
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
1.4.19
|
Updated to Human MSigDB v2022.1.Hs. Direct support for Mouse MSigDB 2022.1.Mm is not yet available
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
1.4.18
|
Updated to MSigDB v7.5.1.
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
1.4.17
|
Updated to MSigDB v7.5.
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
1.4.16
|
Fixed minor typo.
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
1.4.15
|
More flexible CLS parsing.
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
1.4.14
|
Updated for MSigDB v7.4.
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
1.4.13
|
Updated for MSigDB v7.3.
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
1.4.12
|
Updated to MSigDB v7.2.
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
1.4.11
|
Updated to MSigDB v7.1
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
1.4.10
|
Updated to MSigDB v7.0
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
1.4.9
|
Updated to MSigDB v6.2, removed Java dependencies, portability improvements.
|
eby@broadinstitute.org |
GParc (GenePattern Archive)
|
|
|
1.4.6
|
Updated to MSigDB v6.1 (open-access), removed Java dependencies, portability improvements.
|
eby@broadinstitute.org |
GParc (GenePattern Archive)
|
|
|
1.4.4
|
Completed r.package.info edits for awsbatch and rhel6 environments
|
pcarr@broadinstitute.org |
Installed from zip
|
|
|
1.4.2
|
Added Hmisc_3.12-2 dependency to 'r.package.info'
|
pcarr@broadinstitute.org |
Installed from zip
|
|
|
1.2
|
Initial production release.
|
pcarr@broadinstitute.org |
GParc (GenePattern Archive)
|
|
|
|
Convert.Alevin
Read alevin output files and convert them to anndata (.h5ad) or loom (.loom) format for downstream analysis. Designed to convert Alevin Velocity quantification into a compatible format for scVelo.
|
|
|
1
|
Initial Release
|
bhill@broadinstitute.org |
GenePattern production (new)
|
|
|
|
Convert.gmt.to.txt
|
|
|
1
|
|
beltranmm |
Created on server
|
|
|
|
convertcel
|
|
|
1
|
|
mwfoster |
Created on server
|
|
|
|
ConvertLineEndings
Converts line endings to the host operating system's format.
|
|
|
2
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
ConvertToMAGEML
Converts a gct, res, or odf dataset file to a MAGE-ML file
|
|
|
2
|
Fixes bug in the order of the BioDataCube
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
ConvertToMAGETAB
A module to export data from GenePattern in MAGE-TAB format
|
|
|
2
|
Added types for text parameters
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
cool
describe it here
|
|
|
1
|
0
|
Mrohr2016 |
Created on server
|
|
|
|
CopyNumberDivideByNormals
Determines the copy number of a target SNP
|
|
|
3
|
Updated to accept Allele-specific SNP files.
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
CopyNumberFromArray
ZH.Liu
|
|
|
1
|
|
wolfson |
Created on server
|
|
|
|
copyOfComparativeMarkerSelectionViewer
Views the results from ComparativeMarkerSelection
|
|
|
1
|
Bug fix to support S3 files
|
edjuaro |
Created on server
|
|
|
|
copyOfCopyNumberFromArray
ZH.Liu
|
|
|
1
|
|
wolfson |
Created on server
|
|
|
|
copyOfDESeq2
A Differential Expression workflow for RNA-Seq data based on the DESeq2 package from Bioconductor
|
|
|
1
|
Changed to produce a GCT with the normalized counts table. Added a docker image declaration.
|
acastanza |
Created on server
|
|
|
|
copyOfDiagnosticPipeline
|
|
|
1
|
|
atwenzel2 |
Installed from zip
|
|
|
1
|
|
ted |
Installed from zip
|
|
|
|
copyOfGolub.Slonim.1999.Nature.all.aml.pipeline
ALL/AML methodology, from Golub and Slonim et al., 1999
|
|
|
1
|
Modified call to GeneListSignificanceViewer to specify Gene List input file type
|
mmrtest-inf |
Created on server
|
|
|
|
copyOfGolub.Slonim.1999.Nature.all.aml.pipeline
ALL/AML methodology, from Golub and Slonim et al., 1999
|
|
|
1
|
1.0
|
ted |
Created on server
|
|
|
|
copyOfGSEA
Gene Set Enrichment Analysis. <strong>If you are using GSEA on RNA-seq data, please read <a href="http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Using_RNA-seq_Datasets_with_GSEA" target="_blank">these guidelines</a>.</strong>
|
|
|
1
|
10/03/2022 : Updated to Human MSigDB v2022.1.Hs and Mouse MSigDB 2022.1.Mm.
|
ted |
Created on server
|
|
|
|
copyOfHCA_exploratory_pipeline
|
|
|
1
|
|
edwin |
Created on server
|
|
|
|
copyOfMetageneProjection
Projects one or more data sets onto the metagene representation of another data set
|
|
|
1
|
|
acastanza |
Created on server
|
|
|
|
copyOfMultiple_ssGSEA_ROC
Simple_ssGSEA_ROC
|
|
|
7
|
|
TaeHoon5314 |
Created on server
|
|
|
6
|
|
TaeHoon5314 |
Created on server
|
|
|
5
|
|
TaeHoon5314 |
Created on server
|
|
|
4
|
|
TaeHoon5314 |
Created on server
|
|
|
3
|
|
TaeHoon5314 |
Created on server
|
|
|
2
|
|
TaeHoon5314 |
Created on server
|
|
|
1
|
|
TaeHoon5314 |
Created on server
|
|
|
|
copyOfTCGA.SampleSelection
Retrieve TCGA data from Broad FireBrowse and perform sample selection on the basis of expression levels for specific genes of interest for analysis using GSEA tools.
|
|
|
1
|
Update for non-float MSigDB version numbers
|
acastanza |
Created on server
|
|
|
|
copyOfUntitledPipeline3345
|
|
|
1
|
|
ted |
Created on server
|
|
|
|
copyOfUntitledPipeline6041
|
|
|
1
|
|
ted |
Created on server
|
|
|
|
CoxRegression
Cox regression using clinical data and .cls file
|
|
|
3
|
Modified the input.cls.filename parameter to be optional
|
ted |
GenePattern production (new)
|
|
|
2
|
Modified the input.cls.filename parameter to be optional
|
ted |
GenePattern production (new)
|
|
|
1.3
|
Modified the input.cls.filename parameter to be optional
|
pcarr@broadinstitute.org |
Installed from zip
|
|
|
|
CRC_practica.2
describe it here
|
|
|
1
|
0
|
vadrian |
Created on server
|
|
|
|
CreateSymlinks
Creates symlinks to the input files in the job results directory. This is intended to be a helper module for creating scatter-gather pipelines. Note that this module is not supported on Windows
|
|
|
1
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
CsvToFcs
Converts a Comma separated values (CSV) file to a Flow Cytometry Standard (FCS) file.
|
|
|
2
|
Fix for parsing empty keyword values
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
CT60
describe it here
|
|
|
1
|
0
|
supreetagarwal@gmail.com |
Created on server
|
|
|
|
CummeRbund.GeneSetReport
[Beta Release** Contact gp-help with any issues. Check stdout.txt and stderr.txt for errors] Cuffdiff visualization package providing plots based on a user-provided list of genes.
|
|
|
0.21
|
Updated to make use of the R package installer.
|
pcarr@broadinstitute.org |
GenePattern beta
|
|
|
|
CummeRbund.QcReport
[Beta Release** Contact gp-help with any issues. Check stdout.txt and stderr.txt for errors] Cuffdiff visualization package providing plots and tables related to QC and Global Stats.
|
|
|
0.30
|
Updated to make use of the R package installer.
|
pcarr@broadinstitute.org |
GenePattern beta
|
|
|
|
CummeRbund.SelectedConditionsReport
[**Beta Release** Contact gp-help with any issues. Check stdout.txt and stderr.txt for errors] Cuffdiff visualization package providing plots based on a user-provided list of conditions.
|
|
|
0.11
|
Updated to make use of the R package installer.
|
pcarr@broadinstitute.org |
GenePattern beta
|
|
|
|
CummeRbund.SelectedGeneReport
[**Beta Release** Contact gp-help with any issues. Check stdout.txt and stderr.txt for errors] Cuffdiff visualization package providing plots based on a single user-specified gene.
|
|
|
0.17
|
Updated to make use of the R package installer.
|
pcarr@broadinstitute.org |
GenePattern beta
|
|
|
|
CytoHiearchy.
|
|
|
1
|
|
Devansh |
Created on server
|
|
|
|
CytoscapeViewer
Visualizes a gene network
|
|
|
2
|
Updated to Cytoscape 2.5.2
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
D5.vs.iT2
describe it here
|
|
|
1
|
0
|
jwang |
Created on server
|
|
|
|
dapple
describe it here
|
|
|
1
|
0
|
wpongster8 |
Created on server
|
|
|
|
DAPPLE
DAPPLE (Disease Association Protein-Protein Link Evaluator) looks for significant physical connectivity among proteins encoded for by genes in loci associated to disease according to protein-protein interactions reported in the literature.
|
|
|
0.19
|
Official GParc release
|
bhill@broadinstitute.org |
Installed from zip
|
|
|
|
Daryl.Griffin
describe it here
|
|
|
1
|
0
|
darylgriffin |
Created on server
|
|
|
|
Data_Analysis
describe it here
|
|
|
1
|
0
|
Khushbakht |
Created on server
|
|
|
|
DBHeatMapfromGEO
|
|
|
5
|
|
boucherd |
Created on server
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4
|
|
boucherd |
Created on server
|
|
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3
|
|
boucherd |
Created on server
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2
|
|
boucherd |
Created on server
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1
|
|
boucherd |
Created on server
|
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|
|
DE.viewer.
describe it here
|
|
|
1
|
0
|
aakanksha1990 |
Created on server
|
|
|
|
DeIdentifyFCS
DeIdentifyFCS an FCS data file; remove keywords from a list or matching a regular expression; useful to anonymize FCS data files and/or to remove specific (e.g., clinical) information
|
|
|
1
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
delete_copyOfGISTIC_2.0
Genomic Identification of Significant Targets in Cancer (version 2.0.23)
|
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|
1
|
set job.docker.image back to 'genepattern/docker-gistic:0.13'
|
ted |
Created on server
|
|
|
|
delete_me
describe it here
|
|
|
1
|
0
|
ted |
Created on server
|
|
|
|
DESeq2
A Differential Expression workflow for RNA-Seq data based on the DESeq2 package from Bioconductor
|
|
|
3
|
Updated Dockerfile to using R 4.3, updated Deseq2 version as well.
|
edwin5588 |
GenePattern production (new)
|
|
|
2
|
Changed to produce a GCT with the normalized counts table. Added a docker image declaration.
|
ted |
GenePattern production (new)
|
|
|
1
|
Changed to produce a GCT with the normalized counts table. Added a docker image declaration.
|
eby@broadinstitute.org |
Created on server
|
|
|
|
DESeq2.Normalize
A modified version of DESeq2 to perform normalization of RNA-Seq count data without needing to perform differential expression analysis based on the DESeq2 package from Bioconductor
|
|
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2.1
|
|
edjuaro |
Installed from zip
|
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|
|
DESeq2_test
|
|
|
2
|
|
sharonov@gmail.com |
Created on server
|
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1
|
|
sharonov@gmail.com |
Created on server
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DESeq2_test2
|
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3
|
|
sharonov@gmail.com |
Created on server
|
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2
|
|
sharonov@gmail.com |
Created on server
|
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|
1
|
|
sharonov@gmail.com |
Created on server
|
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|
|
DiagnosticPipeline
|
|
|
4
|
|
ted |
Installed from zip
|
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DiagnosticPipeline
|
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|
3
|
|
bkellman |
Installed from zip
|
|
|
2
|
|
bkellman |
Created on server
|
|
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2.1
|
|
bkellman |
Installed from zip
|
|
|
2.0.1
|
|
bkellman |
Installed from zip
|
|
|
1
|
0.1
|
bkellman |
Created on server
|
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|
|
DietSeurat.QC
Seurat quality control (First step in the Seurat Suite), using Seurat version 4.0.3.
|
|
|
1
|
Reading new version of HCA (Loom), fixing the url reading bug (added a new parameter)
|
jonzamora |
Created on server
|
|
|
|
diff
describe it here
|
|
|
1
|
0
|
AnnaCardusFigueras |
Created on server
|
|
|
|
diff_expression
describe it here
|
|
|
2
|
0
|
HUANGSHUAI |
Created on server
|
|
|
1
|
0
|
HUANGSHUAI |
Created on server
|
|
|
|
Differential.expression.Parental
describe it here
|
|
|
1
|
0
|
jayakumar.vadakekolathu2@ntu.ac.uk |
Created on server
|
|
|
|
DifferentialExpressionViewer
Views differential expression results such as from the ComparativeMarkerSelection module. Formerly known as ComparativeMarkerSelectionViewer.
|
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10
|
Renamed from ComparativeMarkerSelectionViewer
|
bhill@broadinstitute.org |
GenePattern production (new)
|
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|
|
DiSCoVER
Beta implementation of the DiSCoVER algorithm.
|
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|
1
|
Displaying the control options as one drop-down menu.
|
edjuaro |
GenePattern production (new)
|
|
|
1.1
|
Showing only upload option for contol.
|
edjuaro |
GenePattern dev
|
|
|
0.4
|
Initial version + fixed an issue with the input format + adding verbosity as an option.
|
edjuaro |
Installed from zip
|
|
|
0.2
|
Initial version + fixed an issue with the input format.
|
edjuaro |
Installed from zip
|
|
|
0.1
|
Initial version
|
edjuaro |
Installed from zip
|
|
|
|
DiseasedHealthy.Mouse.Saliva.
describe it here
|
|
|
3
|
|
acelyaavci |
Created on server
|
|
|
2
|
0
|
acelyaavci |
Created on server
|
|
|
1
|
0
|
acelyaavci |
Created on server
|
|
|
|
DLBCL
describe it here
|
|
|
1
|
0
|
parsas@mskcc.org |
Created on server
|
|
|
|
dna
describe it here
|
|
|
1
|
0
|
Winston |
Created on server
|
|
|
|
DOWNINGwwo
describe it here
|
|
|
1
|
0
|
dshin |
Created on server
|
|
|
|
download
describe it here
|
|
|
1
|
0
|
guest_101923 |
Created on server
|
|
|
|
DownloadURL
Downloads a file from a URL
|
|
|
1
|
Added email address to owner contact
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
duh
describe it here
|
|
|
1
|
0
|
Diamond |
Created on server
|
|
|
|
DW_training
training
|
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1
|
|
dwang326 |
Created on server
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eadj
|
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|
1
|
|
alberto.peloso2 |
Created on server
|
|
|
|
early_versus_primary
describe it here
|
|
|
1
|
0
|
mschue |
Created on server
|
|
|
|
echo
echo test
|
|
|
5
|
|
ted |
Installed from zip
|
|
|
|
echo_userdir
testuserdir
|
|
|
1
|
|
ted |
Created on server
|
|
|
|
edwinharm
Harmony is a batch correction tool. Upon use, this module will produce three scatterplots. One plot will show the data pre-Harmony, and can be found in the 'BeforeHarmonyPlot.png' file. In this plot, the x and y axes represent the 1st and 2nd principal components from PCA dimensional reduction (unless specified otherwise by the user). Another plot will show the data post-Harmony, and can be found in the 'AfterHarmonyPlot.png' file. In this plot, the x and y axes the same dimensions used in the pre-Harmony plot are shown, but adjusted by Harmony. Lastly, the third plot shows the pre-Harmony and post-Harmony plots side by side for comparison.
|
|
|
1
|
Added batch correction tag
|
edwin5588 |
Created on server
|
|
|
|
EGF.WT.
describe it here
|
|
|
1
|
0
|
jvannostrand |
Created on server
|
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|
|
eleonora
|
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|
1
|
|
vercesie |
Created on server
|
|
|
|
EMT
describe it here
|
|
|
1
|
0
|
Hazafa |
Created on server
|
|
|
|
Esercitazione
|
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5
|
|
Giuseppe.serio01 |
Created on server
|
|
|
4
|
|
Giuseppe.serio01 |
Created on server
|
|
|
3
|
|
Giuseppe.serio01 |
Created on server
|
|
|
2
|
|
Giuseppe.serio01 |
Created on server
|
|
|
1
|
|
Giuseppe.serio01 |
Created on server
|
|
|
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esercitazione3
|
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1
|
|
carolina.bo |
Created on server
|
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esercitazione_magni
|
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1
|
|
carolina94 |
Created on server
|
|
|
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Esercitazione_MattiaChiesa
|
|
|
2
|
|
MiriamA |
Created on server
|
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|
1
|
|
MiriamA |
Created on server
|
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|
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Esercitazione_MattiaChiesa
|
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|
1
|
|
MiriamA |
Created on server
|
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EsercitazioneChiesa
|
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|
1
|
|
MiriamA |
Created on server
|
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EsercitazioneNGS
|
|
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1
|
|
MiriamA |
Created on server
|
|
|
|
ESPPredictor
Determine which tryptic peptides will generate the highest signal in ESI-MS
|
|
|
4
|
Dockerized release
|
bhill@broadinstitute.org |
GenePattern production (new)
|
|
|
|
esrcitazione
|
|
|
2
|
|
carolina94 |
Created on server
|
|
|
1
|
|
carolina94 |
Created on server
|
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ESub
|
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|
1
|
|
alberto.peloso |
Created on server
|
|
|
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esub
|
|
|
1
|
|
alberto.peloso2 |
Created on server
|
|
|
|
esub2
|
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|
1
|
|
alberto.peloso2 |
Created on server
|
|
|
|
ex1
describe it here
|
|
|
1
|
0
|
TasneemArsiwala |
Created on server
|
|
|
|
Ex4_preprocessing
Pipeline for GenePattern based preprocessing of GSE635 data.
|
|
|
1.7
|
v.0.4
|
jj.chrzanowski1 |
Installed from zip
|
|
|
1.7
|
v.0.4
|
botomj@gmail.com |
Installed from zip
|
|
|
1.7
|
v.0.4
|
botomj |
Installed from zip
|
|
|
1.7
|
v.0.4
|
jedrzej.chrzanowski |
Installed from zip
|
|
|
1.6
|
v.0.3
|
jedrzej.chrzanowski |
Created on server
|
|
|
1.5
|
v.0.3
|
jj.chrzanowski1 |
Installed from zip
|
|
|
1.5
|
v.0.3
|
jedrzej.chrzanowski |
Installed from zip
|
|
|
1.4
|
v.0.2
|
jedrzej.chrzanowski |
Created on server
|
|
|
1.3
|
v.0.1
|
jedrzej.chrzanowski |
Created on server
|
|
|
|
Example
Example1
|
|
|
1
|
|
GuadalupeAntonio |
Created on server
|
|
|
|
Example_for_PTSP
describe it here
|
|
|
1
|
0
|
ted |
Created on server
|
|
|
|
example_mutsig
|
|
|
2
|
|
ab12kim |
Created on server
|
|
|
1
|
|
ab12kim |
Created on server
|
|
|
|
explore
describe it here
|
|
|
1
|
0
|
mital14 |
Created on server
|
|
|
|
ExpressionFileCreator
Creates a RES or GCT file from a set of Affymetrix CEL files. For IVT arrays only; use AffySTExpressionFileCreator for ST arrays.
|
|
|
12.5
|
include R packages in container and fix for stderr output of install.packages(<repos_cdf>)
|
pcarr@broadinstitute.org |
https://modulerepository.genepattern.org/gpModuleRepository//?env=dev
|
|
|
12.4.1
|
installed R packages in container, job.docker.image='genepattern/expressionfilecreator:v12.4.1'
|
pcarr@broadinstitute.org |
Installed from zip
|
|
|
12.3
|
Updated to make use of the R package installer. Fixes a bug in failing to remove downloaded annotation files.
|
pcarr@broadinstitute.org |
GenePattern beta
|
|
|
|
ExprToGct
Converts an EXPR file to GCT format
|
|
|
2
|
Fixed handling of different newline characters
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
ExtractColumnNames
Lists the sample descriptors from a .res file.
|
|
|
2
|
Annotated for GP 1.4
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
ExtractComparativeMarkerResults
Creates a derived dataset and feature list file from the results of ComparativeMarkerSelection
|
|
|
4
|
Renamed field parameter to statistic
|
pcarr@broadinstitute.org |
Installed from zip
|
|
|
2
|
Adds ability to extract top features by score
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
extractcompmarker
describe it here
|
|
|
2
|
0
|
robynm |
Created on server
|
|
|
1
|
0
|
robynm |
Created on server
|
|
|
|
ExtractFCSDataset
Extract one or more FCS datasets from an FCS data file
|
|
|
2
|
Updated to include more lenient CFCS library
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
ExtractFCSKeywords
Extracts keyword(s) value(s) from a Flow Cytometry Standard (FCS) file.
|
|
|
2
|
Updated to release candidate from Josef which includes more lenient CFCS library
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
ExtractFCSParameters
Extract specified parameters (dimensions) from an FCS data file.
|
|
|
2
|
Fix for parsing empty keyword values
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
ExtractRowNames
Extracts the row names from a .res, .gct, or .odf file.
|
|
|
3
|
Added support for gct and odf files
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
EYE.GCT
describe it here
|
|
|
1
|
0
|
libai |
Created on server
|
|
|
|
FastQC
Provides quality control metrics on raw sequence data
|
|
|
1
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
0.5
|
|
pcarr@broadinstitute.org |
GenePattern beta
|
|
|
|
FastqToBAM
|
|
|
1
|
|
joller |
Created on server
|
|
|
|
FCS.to.Cell.matrix
|
|
|
1
|
|
pmcerlean1 |
Created on server
|
|
|
|
FCS_Version_Conversion
Converts FCS files to CSV and back to allow programs to read FCS files from FACSDiVa
|
|
|
1
|
|
AbidingProduce |
Created on server
|
|
|
|
FCS_Version_Correction
Converts FCS files to CSV and back to FCS to allow programs to utilize unsupported FCS versions.
|
|
|
1
|
|
AbidingProduce |
Created on server
|
|
|
|
FcsToCsv
Converts a Flow Cytometry Standard (FCS) file to a Comma Separated Values (CSV) file.
|
|
|
3
|
Added fix for parsing empty keyword values
|
pcarr@broadinstitute.org |
GenePattern dev
|
|
|
|
FeatureSummaryViewer
Feature Summary Viewer
|
|
|
4
|
Updated GeneCruiser library
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
1
|
includes an interactive histogram of the features included in each cross validation run and includes interactive annotation of Affy probe IDs using GeneCruiser.
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
ff
describe it here
|
|
|
1
|
0
|
firoz |
Created on server
|
|
|
|
fff
describe it here
|
|
|
2
|
0
|
xjyang1974 |
Created on server
|
|
|
1
|
0
|
xjyang1974 |
Created on server
|
|
|
|
File1_SeqCounts
describe it here
|
|
|
1
|
0
|
arichi |
Created on server
|
|
|
|
FileSplitter
Splits a file into equal-sized chunks, given the number of lines per output file
|
|
|
2
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
FilterFilelist
a helper module which generates a filtered filelist from the input filelist and some filter parameters.
|
|
|
1
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
First.try
describe it here
|
|
|
1
|
0
|
darshininambiar@gmail.com |
Created on server
|
|
|
|
First.try.012223
describe it here
|
|
|
1
|
0
|
21chuck |
Created on server
|
|
|
|
FLAMEPreprocess
Performs preprocessing of .fcs or .txt flow cytometric data files
|
|
|
4.2
|
Pin common.R to the one associated with v. 4 release of this module
|
pcarr@broadinstitute.org |
GenePattern beta
|
|
|
|
focais.
describe it here
|
|
|
1
|
0
|
Elisabete |
Created on server
|
|
|
|
foofoo
describe it here
|
|
|
1
|
0
|
ted |
Created on server
|
|
|
|
FP_HC2978
|
|
|
1
|
|
jbzhang |
Created on server
|
|
|
|
Fpkm_trackingToGct
Takes a Cufflinks FPKM_tracking file and converts it to GCT format.
|
|
|
5
|
Updated to output scientific values and 0s as output by Cufflinks
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
FPKMUQ1500_12042018
|
|
|
1
|
|
lydia.lam |
Created on server
|
|
|
|
g
describe it here
|
|
|
1
|
0
|
HUANGSHUAI |
Created on server
|
|
|
|
GBM_htseq_count
describe it here
|
|
|
1
|
0
|
Saleem |
Created on server
|
|
|
|
gct
describe it here
|
|
|
1
|
0
|
CHOIHEEJUNG |
Created on server
|
|
|
|
gct.file
describe it here
|
|
|
1
|
0
|
16tcv |
Created on server
|
|
|
|
GctToPcl
Convert .gct to .pcl
|
|
|
1
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
GDS6083
describe it here
|
|
|
1
|
0
|
fzgabo |
Created on server
|
|
|
|
gene.analysis
describe it here
|
|
|
1
|
0
|
MoeezAhmed |
Created on server
|
|
|
|
gene_expression
|
|
|
1
|
|
alison_lee |
Created on server
|
|
|
|
GeneListAll
|
|
|
5
|
|
yiwenh |
Created on server
|
|
|
4
|
|
yiwenh |
Created on server
|
|
|
3
|
|
yiwenh |
Created on server
|
|
|
2
|
|
yiwenh |
Created on server
|
|
|
1
|
|
yiwenh |
Created on server
|
|
|
|
GeneListSignificanceViewer
Views the results of marker analysis
|
|
|
4
|
Updated GeneCruiser library
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
2
|
includes interactive plots and annotation of Affymetrix probe identifiers
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
GeneNeighbors
Select genes that most closely resemble a continuous profile (e.g., another gene)
|
|
|
4
|
updated thresholds to post-2002 Affy Values
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
geneSelect_12042018
|
|
|
1
|
|
lydia.lam |
Created on server
|
|
|
|
genetic
describe it here
|
|
|
1
|
0
|
Winston |
Created on server
|
|
|
|
Genomespace
describe it here
|
|
|
1
|
0
|
BrunoLarrivee |
Created on server
|
|
|
|
GEOImporter
Imports data from the Gene Expression Omnibus (GEO)
|
|
|
6
|
Updated NCIBI FTP paths. Added ability to omit rows with all NA values. Updated to use R 4.0.3 via module specific Docker container.
|
bhill@broadinstitute.org |
Created on server
|
|
|
|
GFP.exo.1.file.1.R1
describe it here
|
|
|
1
|
0
|
thepreztonlee |
Created on server
|
|
|
|
GFP_exo_1_S24_L001_R1_001.fastq
describe it here
|
|
|
1
|
0
|
thepreztonlee |
Created on server
|
|
|
|
gg
describe it here
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1
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0
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yungminc12 |
Created on server
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gistic
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2
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tothr |
Created on server
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1
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tothr |
Created on server
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GISTIC.1
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1
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chuting |
Created on server
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gistic2
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1
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dyy |
Created on server
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GISTIC2_lymph_hisens_adjusted
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2
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dutian |
Created on server
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1
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dutian |
Created on server
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GISTIC_2.0
Genomic Identification of Significant Targets in Cancer (version 2.0.23)
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6.15.30
|
Fixed remove.X
|
tabor |
Installed from zip
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6.15.28
|
Fixing Docker container
|
tabor |
Installed from zip
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6.15.21
|
added the rest of the v6.14 hard-coded args back to the command line
|
pcarr-dev |
Installed from zip
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6.15.20
|
add '-genepattern 1' back to the command line
|
pcarr-dev |
Installed from zip
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6.15.19
|
updated command line args to match the 2.0.23 example
|
pcarr-dev |
Installed from zip
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6.15.18
|
updated command line args to match the 2.0.23 example
|
pcarr-dev |
Installed from zip
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6.15.17
|
updated command line args to match the 2.0.23 example
|
pcarr-dev |
Installed from zip
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6.15.16
|
set prefix_when_specified for 'remove.X', removed default value
|
pcarr-dev |
Installed from zip
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6.15.15
|
removed '-savedata 0' command line arg
|
pcarr-dev |
Installed from zip
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6.15.11
|
refactor, commandLine format in manifest file
|
pcarr-dev |
Installed from zip
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6.15.10
|
make 'output.prefix' an optional parameter
|
pcarr-dev |
Installed from zip
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6.15.9
|
set job.docker.image to 'genepattern/docker-gistic:0.13'
|
pcarr-dev |
Installed from zip
|
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6.15.8
|
commandLine=gp_gistic2_from_seg ..., 'genepattern/docker-gistic:latest'
|
pcarr@broadinstitute.org |
Installed from zip
|
|
|
6.15.7
|
commandLine=runMatlab.sh gp_gistic2_from_seg ..., runMatlab.sh initializes the environment in the container
|
pcarr@broadinstitute.org |
Installed from zip
|
|
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6.15.4
|
Containerized GISTIC v2.0.23, set job.docker.image='genepattern/docker-gistic:0.11, gp_gistic2_from_seg cmd in libdir'
|
pcarr@broadinstitute.org |
Installed from zip
|
|
|
6.14
|
Updated to GISTIC v2.0.23, added '-maxspace' and '-logdat' params, no longer requires a markers file
|
bhill@broadinstitute.org |
GenePattern production (new)
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GISTIC_2.0_default.TCGA
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3
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vlkjvlkj |
Created on server
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2
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vlkjvlkj |
Created on server
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1
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vlkjvlkj |
Created on server
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GISTIC_2defaultTCGA
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2
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vlkjvlkj |
Created on server
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1
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vlkjvlkj |
Created on server
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GISTIC_Canfam
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1
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hhyunji1027@naver.com |
Created on server
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GISTIC_ESCC
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2
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chuting |
Created on server
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1
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chuting |
Created on server
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GISTIC_test_1
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4
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justin28969 |
Created on server
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3
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justin28969 |
Created on server
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2
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justin28969 |
Created on server
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1
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justin28969 |
Created on server
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GlobalAlignment
standard global sequence analysis
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0
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|
pcarr@broadinstitute.org |
GenePattern production (new)
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Golub.Slonim.1999.Nature.all.aml.pipeline
ALL/AML methodology, from Golub and Slonim et al., 1999
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3
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ted |
Installed from zip
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2
|
Modified call to GeneListSignificanceViewer to specify Gene List input file type
|
pcarr@broadinstitute.org |
GenePattern production (new)
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|
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Golub.Slonim.all.aml.pipeline
ALL/AML methodology, from Golub and Slonim et al., 1999
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1
|
Modified call to GeneListSignificanceViewer to specify Gene List input file type
|
mmrtest5 |
Created on server
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GR.resting
describe it here
|
|
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1
|
0
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zhliusalk |
Created on server
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gse
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1
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inaselsayed |
Created on server
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GSE273726_naivevmemory_genep
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1
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guest_100489 |
Created on server
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GSE273726_naivevmemory_genep
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1
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|
guest_100489 |
Created on server
|
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GSE273726_naivevmemory_genep
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1
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|
guest_100489 |
Created on server
|
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|
GSEA
Gene Set Enrichment Analysis. <strong>If you are using GSEA on RNA-seq data, please read <a href="http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Using_RNA-seq_Datasets_with_GSEA" target="_blank">these guidelines</a>.</strong>
|
|
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20.4.0
|
10/03/2022 : Updated to Human MSigDB v2022.1.Hs and Mouse MSigDB 2022.1.Mm.
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
20.3.6
|
09/15/2022 : Updated to Human MSigDB v2022.1.Hs. Direct support for Mouse MSigDB 2022.1.Mm is not yet available
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
20.3.5
|
03/02/2022 : Removed Log4J entirely from the code base. Fixed weighted_p1.5 computation. Added min dataset size warnings.
|
eby@broadinstitute.org |
GenePattern production (new)
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|
gsea.jurkat
describe it here
|
|
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1
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0
|
marsluo |
Created on server
|
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GSEA.KRAS
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1
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okondrashova |
Created on server
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GSEA.pipe
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10
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maya3 |
Created on server
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9
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maya3 |
Created on server
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9.1
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maya3 |
Created on server
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8
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maya3 |
Created on server
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7
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maya3 |
Created on server
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6
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maya3 |
Created on server
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GSEA_Norm
describe it here
|
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6
|
0
|
liuh |
Created on server
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5
|
0
|
liuh |
Created on server
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4
|
0
|
liuh |
Created on server
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GSEA_rnk
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1
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rluchtel |
Created on server
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gsea_tex
describe it here
|
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1
|
0
|
pjuszczynski@ihit.waw.pl |
Created on server
|
|
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GSEA_Unt_Il22KO_v_WT
describe it here
|
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1
|
0
|
omershomrat |
Created on server
|
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GSEALeadingEdge
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1
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|
BWilde@mednet.ucla.edu |
Created on server
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GSEALeadingEdge2
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1
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|
BWilde@mednet.ucla.edu |
Created on server
|
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GSEALeadingEdgeViewer
Leading Edge Viewer for GSEA results
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|
|
6
|
Updated to the GSEA 4.2.3 code base, removing Log4J entirely from the code base.
|
eby@broadinstitute.org |
GenePattern production (new)
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GSEApreranked
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3
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jingranhao |
Created on server
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2
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jingranhao |
Created on server
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1
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|
jingranhao |
Created on server
|
|
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GSEAPreranked
Runs the gene set enrichment analysis against a user-supplied ranked list of genes.
|
|
|
7.4.0
|
10/03/2022 : Fixed a manifest typo. Updated to Human MSigDB v2022.1.Hs. Direct support for Mouse MSigDB 2022.1.Mm is not yet available
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
7.3.7
|
09/26/2022 : Fixed a manifest typo. Updated to Human MSigDB v2022.1.Hs. Direct support for Mouse MSigDB 2022.1.Mm is not yet available
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
7.3.5
|
03/02/2022 : Removed Log4J entirely from the code base. Fixed weighted_p1.5 computation. Added min dataset size warnings.
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
|
GYG1
describe it here
|
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1
|
0
|
cornelius |
Created on server
|
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H.part
describe it here
|
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1
|
0
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jaeryunryu |
Created on server
|
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Harmony
Harmony is a batch correction tool. Upon use, this module will produce three scatterplots. One plot will show the data pre-Harmony, and can be found in the 'BeforeHarmonyPlot.png' file. In this plot, the x and y axes represent the 1st and 2nd principal components from PCA dimensional reduction (unless specified otherwise by the user). Another plot will show the data post-Harmony, and can be found in the 'AfterHarmonyPlot.png' file. In this plot, the x and y axes the same dimensions used in the pre-Harmony plot are shown, but adjusted by Harmony. Lastly, the third plot shows the pre-Harmony and post-Harmony plots side by side for comparison.
|
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6
|
changed default values to be blank
|
edwin5588 |
GenePattern production (new)
|
|
|
3
|
Added batch correction tag
|
edwin5588 |
GenePattern production (new)
|
|
|
2
|
Added animations
|
edwin5588 |
GenePattern production (new)
|
|
|
2.1
|
Added batch correction tag
|
edwin5588 |
GenePattern dev
|
|
|
1
|
Removed dockerhub tag and reference from description
|
edwin5588 |
GenePattern production (new)
|
|
|
|
HC
describe it here
|
|
|
1
|
0
|
larissa.cassiano |
Created on server
|
|
|
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HCA_exploratory_pipeline
|
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|
1
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edwin |
Created on server
|
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HCA_pipe2
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2
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|
edwin |
Created on server
|
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1
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|
edwin |
Created on server
|
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HCA_pipe2
|
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1
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edjuaro |
Created on server
|
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heat
describe it here
|
|
|
1
|
0
|
harris@uthscsa.edu |
Created on server
|
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|
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heat.map
describe it here
|
|
|
2
|
0
|
16tcv |
Created on server
|
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1
|
0
|
16tcv |
Created on server
|
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|
|
Heat.Map.
describe it here
|
|
|
3
|
|
eanderson34 |
Created on server
|
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2
|
0
|
eanderson34 |
Created on server
|
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1
|
0
|
eanderson34 |
Created on server
|
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|
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heatmap
describe it here
|
|
|
3
|
0
|
fkipper |
Created on server
|
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2
|
0
|
fkipper |
Created on server
|
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1
|
0
|
fkipper |
Created on server
|
|
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1.1
|
0
|
fkipper |
Created on server
|
|
|
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heatmap
describe it here
|
|
|
1
|
0
|
JeffLiu |
Created on server
|
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|
|
heatmap
describe it here
|
|
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1
|
0
|
JeffLiu |
Created on server
|
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|
|
heatmap
describe it here
|
|
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1
|
0
|
JeffLiu |
Created on server
|
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|
|
HEATMAP
describe it here
|
|
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1
|
0
|
ramaniganesh |
Created on server
|
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|
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Heatmap
describe it here
|
|
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1
|
0
|
Ekaterina |
Created on server
|
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|
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Heatmap
describe it here
|
|
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1
|
0
|
16tcv |
Created on server
|
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|
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Heatmap.generation
describe it here
|
|
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1
|
0
|
joannahfergusson |
Created on server
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Heatmap.generator.
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2
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|
eanderson34 |
Created on server
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1
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|
eanderson34 |
Created on server
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1.2
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|
eanderson34 |
Created on server
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1.1
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|
eanderson34 |
Created on server
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HeatMapImage
Creates a heat map from a dataset
|
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6
|
Fixed bug in discrete color scheme. Added gradient color scheme option.
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
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HeatMapViewer
A configurable heat map viewer that provides users with several options for manipulating and visualizing array-based data
|
|
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13
|
Updated to improve compatibility with Java 7 security updates
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
13.11
|
Bug fix to support S3 files
|
tabor |
GenePattern production (new)
|
|
|
13.9
|
Initial beta release
|
pcarr@broadinstitute.org |
GenePattern beta
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HGS_CCLE_DepMap_EMT_hallmarks
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1
|
|
greta.gudoityt |
Created on server
|
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HierarchicalClustering
Hierarchical Clustering
|
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|
6
|
Updated for Java 7
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
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HierarchicalClustering_image
|
|
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1
|
|
gwang6@mdanderson.org |
Created on server
|
|
|
|
HierarchicalClusteringImage
Creates an image of the dendrogram generated from HierarchicalClustering
|
|
|
4
|
removed non-functional rows to highlight parameter, removed invalid .esp output option, added genepattern/docker-java17:0.12 to manifest
|
bhill@broadinstitute.org |
GenePattern production (new)
|
|
|
3
|
Fixed row/column size transposing
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
HierarchicalClusteringPipeline
HierarchicalClustering
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|
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2
|
|
harbison |
Created on server
|
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1
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|
harbison |
Created on server
|
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|
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HierarchicalClusteringViewer
Views results of hierarchical clustering.
|
|
|
11.5
|
Bug fix for S3 files
|
tabor |
GenePattern production (new)
|
|
|
11.3
|
Converted to Javascript implementation - initial beta release
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
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high
|
|
|
30
|
|
chuting |
Created on server
|
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29
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chuting |
Created on server
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28
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chuting |
Created on server
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27
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chuting |
Created on server
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26
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chuting |
Created on server
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25
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chuting |
Created on server
|
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24
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chuting |
Created on server
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23
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chuting |
Created on server
|
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22
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chuting |
Created on server
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21
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chuting |
Created on server
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20
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chuting |
Created on server
|
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19
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chuting |
Created on server
|
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18
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chuting |
Created on server
|
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17
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chuting |
Created on server
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16
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chuting |
Created on server
|
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15
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chuting |
Created on server
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14
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chuting |
Created on server
|
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13
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|
chuting |
Created on server
|
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12
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|
chuting |
Created on server
|
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11
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|
chuting |
Created on server
|
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10
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|
chuting |
Created on server
|
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9
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|
chuting |
Created on server
|
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8
|
|
chuting |
Created on server
|
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7
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|
chuting |
Created on server
|
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6
|
|
chuting |
Created on server
|
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|
5
|
|
chuting |
Created on server
|
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4
|
|
chuting |
Created on server
|
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3
|
|
chuting |
Created on server
|
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2
|
|
chuting |
Created on server
|
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1
|
|
chuting |
Created on server
|
|
|
|
HISAT2.aligner
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).
|
|
|
3
|
Changed index dynamic source from ftp://gpft p to the copy on https://datasets.genepattern.org
|
ted |
GenePattern production (new)
|
|
|
2
|
Changed index dynamic source from ftp://gpft p to the copy on https://datasets.genepattern.org
|
ted |
GenePattern production (new)
|
|
|
1
|
|
bhill@broadinstitute.org |
Created on server
|
|
|
1.6
|
Changed index dynamic source from ftp://gpft p to the copy on https://datasets.genepattern.org
|
ted |
GenePattern dev
|
|
|
1.5
|
Updated name and doc location
|
bhill@broadinstitute.org |
GenePattern production (new)
|
|
|
|
HISAT2Indexer
Indexes one or more FASTA files for use in the HISAT2Aligner.
|
|
|
1
|
|
bhill@broadinstitute.org |
Created on server
|
|
|
1.9
|
Updating module name and doc location
|
bhill@broadinstitute.org |
GenePattern production (new)
|
|
|
|
HM
describe it here
|
|
|
2
|
0
|
giusy.dellagatta |
Created on server
|
|
|
1
|
0
|
giusy.dellagatta |
Created on server
|
|
|
|
HTSeq.Count
Takes alignment files in SAM/BAM format and a feature file in GTF/GFF format (usually with exon annotation), name sorts the alignment file and calculates for each sample the number of reads mapping to each feature. (HTSeq.count v0.11.2)
|
|
|
4
|
Modified to use datasets.genepattern.org instead of ftp://gpftp.broadinstitutue.org as source for default gtf files
|
ted |
GenePattern production (new)
|
|
|
3
|
Beta release
|
bhill@broadinstitute.org |
GenePattern production (new)
|
|
|
3.1
|
Modified to use datasets.genepattern.org instead of ftp://gpftp.broadinstitutue.org as source for default gtf files
|
ted |
GenePattern dev
|
|
|
|
httpsdatasets.genepattern.orgdataall_amlall_aml_train.gct.
describe it here
|
|
|
2
|
0
|
Naiaradaris |
Created on server
|
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1
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0
|
Naiaradaris |
Created on server
|
|
|
|
httpsdatasets.genepattern.orgdataall_amlall_aml_train.gct.
describe it here
|
|
|
1
|
0
|
guest_100230 |
Created on server
|
|
|
|
httpsdatasets.genepattern.orgdataall_amlall_aml_train.gct.
describe it here
|
|
|
1
|
0
|
guest_100230 |
Created on server
|
|
|
|
httpsdatasets.genepattern.orgdataall_amlarchiveall_aml_train.res
describe it here
|
|
|
1
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0
|
Sruthi S |
Created on server
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|
|
|
Hu68kHu35kAtoU95
Converts a list of Affymetrix Hu6800/Hu35KsubA probes to the corresponding Affymetrix U95Av2 probes.
|
|
|
1
|
Updated documentation
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
Human_GRCh37_hg19.fasta.gz
describe it here
|
|
|
1
|
0
|
Nattawan |
Created on server
|
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|
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HumanData
describe it here
|
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2
|
0
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16tcv |
Created on server
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1
|
0
|
16tcv |
Created on server
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HW1
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2
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|
Longwei |
Created on server
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1
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|
Longwei |
Created on server
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hw1
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3
|
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ntduong555 |
Created on server
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2
|
|
ntduong555 |
Created on server
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1
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|
ntduong555 |
Created on server
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hw2155
|
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2
|
|
ntduong555 |
Created on server
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1
|
|
ntduong555 |
Created on server
|
|
|
|
ibru
describe it here
|
|
|
1
|
0
|
Margaret_H |
Created on server
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|
|
Ident_Vis_RNAseq_data
|
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1
|
|
rmiller@med.unc.edu |
Created on server
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|
|
Ignacio.y.Estefania
describe it here
|
|
|
1
|
0
|
fannyemg9 |
Created on server
|
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|
|
Igor_clustering
|
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1
|
|
IgorShats |
Created on server
|
|
|
|
igv.js
Launches igv.js with input file(s)
|
|
|
2.5
|
Bug fix for S3 files
|
tabor |
GenePattern production (new)
|
|
|
2.4
|
Bug fix for optional locus parameter when run from notebook
|
bhill@broadinstitute.org |
GenePattern production (new)
|
|
|
2.1
|
Updated to igv.js v2.3.5
|
tabor |
GenePattern production (new)
|
|
|
|
il1
describe it here
|
|
|
1
|
0
|
heba ismail |
Created on server
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|
|
ilker
|
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1
|
|
ilkeraltundas |
Created on server
|
|
|
|
IlluminaExpressionFileCreator
Creates a GCT file from a zip of Illumina IDAT files and an Illumina manifest file
|
|
|
2
|
Improved handling of manifests and zip files; removed required string "_Grn" in input filenames
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
IlluminaPipeline
|
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|
1
|
|
mmrtest5 |
Created on server
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|
|
Immunome
describe it here
|
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1
|
0
|
PAGLIUS |
Created on server
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|
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improveFigure
describe it here
|
|
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1
|
0
|
snharbi |
Created on server
|
|
|
|
ImputeMissingValues.KNN
Imputes missing values
|
|
|
13
|
Renamed module from ImputeMissingValues.KNN to ImputeMissingValuesKNN
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
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|
|
Index
describe it here
|
|
|
1
|
0
|
seoyoungee |
Created on server
|
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|
|
IR
describe it here
|
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|
1
|
0
|
wenbin-yang@northwestern.edu |
Created on server
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|
|
IRpipeline
describe it here
|
|
|
1
|
0
|
blb74 |
Created on server
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|
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Isoform.quantification
|
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3
|
|
alekszakirov |
Created on server
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2
|
|
alekszakirov |
Created on server
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1
|
|
alekszakirov |
Created on server
|
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|
|
j
describe it here
|
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|
1
|
0
|
upvgenomica |
Created on server
|
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|
|
JavaTreeView
Hierarchical clustering viewer that reads in Eisen's cdt, atr, and gtr files. A detailed description of these formats is available from http://microarray.ccgb.umn.edu/smd/html/MicroArray/help/formats.shtml
|
|
|
2
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
javi
describe it here
|
|
|
1
|
0
|
jabemo |
Created on server
|
|
|
|
JM
describe it here
|
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2
|
0
|
john.manion |
Created on server
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1
|
0
|
john.manion |
Created on server
|
|
|
|
Jurkat
describe it here
|
|
|
1
|
0
|
ccagle |
Created on server
|
|
|
|
Kallisto.Indexer
Builds an index from a FASTA formatted file of target sequences for use with Kallisto.
|
|
|
2
|
add documentation, author, docker, source code repo, change visibility to public, quality level to preproduction
|
ted |
GenePattern production (new)
|
|
|
1
|
add documentation, author, docker, source code repo, change visibility to public, quality level to preproduction
|
edwin5588 |
GenePattern production (new)
|
|
|
|
Kallisto.Quant
Runs Kallisto to perform pseudoalignment (using a human or mouse transcriptome index) and gene-level aggregation
|
|
|
4
|
dynamic drop down for kallisto, rename to Kallisto.Quant, update parameter descriptions
|
edwin5588 |
GenePattern production (new)
|
|
|
3
|
Exposing all Kallisto parameters
|
tabor |
GenePattern production (new)
|
|
|
2
|
Added Mouse index, Release M26 (GRCm39), and updated Human index, Release 37 (GRCh38.p13), from Gencode.
|
tabor |
GenePattern production (new)
|
|
|
1
|
Initial version (1.0)
|
edjuaro |
GenePattern production (new)
|
|
|
0.1
|
Initial version
|
edjuaro |
GenePattern production (new)
|
|
|
|
kkk
describe it here
|
|
|
1
|
0
|
Wallax |
Created on server
|
|
|
|
kmean.cluster
describe it here
|
|
|
1
|
0
|
ychmax8@gmail.com |
Created on server
|
|
|
|
kmeans
describe it here
|
|
|
1
|
0
|
monser9610 |
Created on server
|
|
|
|
KMeansClustering
Module that performs the K-Means Clustering algorithm
|
|
|
2
|
Fixed listing of acceptable input file formats
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
KNN
K-nearest neighbors classification
|
|
|
4
|
Set default distance measure to Euclidean
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
2
|
Added ability to save prediction model
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
KNN_pipeline_cc_noncc
|
|
|
1
|
|
alsawao |
Created on server
|
|
|
|
KNNXValidation
KNN classification with Leave-One-Out Cross-Validation
|
|
|
6
|
Set default value of distance measure to Euclidean
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
KSscore
Computes the Kolmogorov-Smirnov score for a set of genes within an ordered list.
|
|
|
1
|
Added email address to owner contact
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
l
describe it here
|
|
|
1
|
0
|
lbaert |
Created on server
|
|
|
|
l
describe it here
|
|
|
1
|
0
|
rakangxxx |
Created on server
|
|
|
|
LA38
describe it here
|
|
|
1
|
0
|
LameesAb |
Created on server
|
|
|
|
LandmarkMatch
A proteomics method to propogate identifed peptides across multiple MS runs
|
|
|
2
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
LCMmicroarray
describe it here
|
|
|
1
|
0
|
jxy953 |
Created on server
|
|
|
|
Line
describe it here
|
|
|
1
|
0
|
lamantiamaria@gmail.com |
Created on server
|
|
|
|
line1
|
|
|
1
|
|
chuting |
Created on server
|
|
|
|
line2
|
|
|
1
|
|
chuting |
Created on server
|
|
|
|
ListFiles
a helper module which outputs a filelist, the list of all files in the input directory, similar to the unix 'ls' command
|
|
|
0.3
|
Updated source code to use FindCommand and FileVisitor pattern
|
pcarr@broadinstitute.org |
GenePattern beta
|
|
|
|
liuzaoqu
describe it here
|
|
|
2
|
0
|
liuzaoqu |
Created on server
|
|
|
1
|
0
|
liuzaoqu |
Created on server
|
|
|
|
Liya.Ding
describe it here
|
|
|
3
|
0
|
WilliamHou |
Created on server
|
|
|
2
|
0
|
WilliamHou |
Created on server
|
|
|
1
|
0
|
WilliamHou |
Created on server
|
|
|
|
LocatePeaks
Locates detected peaks in a spectrum.
|
|
|
2
|
Updated for R 2.5.0
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
log
describe it here
|
|
|
2
|
0
|
hwichova |
Created on server
|
|
|
1
|
0
|
hwichova |
Created on server
|
|
|
|
LogicleTransformFCS
Logicle transformation of (selected) parameters in a list mode FCS data file.
|
|
|
1
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
LogTransform
og transform a data (gct) file.
|
|
|
3
|
Initial version
|
edjuaro |
Created on server
|
|
|
2
|
Initial version
|
edjuaro |
Created on server
|
|
|
1
|
Initial version
|
edjuaro |
Created on server
|
|
|
|
logTransform
asdf
|
|
|
2
|
|
ted |
Installed from zip
|
|
|
|
LogTransformEdwinTest
Log transform a data (gct) file.
|
|
|
3
|
Initial version
|
edjuaro |
Created on server
|
|
|
2
|
Initial version
|
edjuaro |
Created on server
|
|
|
1
|
Initial version
|
edjuaro |
Created on server
|
|
|
|
LOHPaired
Computes LOH for paired samples
|
|
|
3
|
Pairings based on array name instead of sample name
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
LOOCV_SurvivalSignature
Train a predictive molecular signature for time-to-event outcome with censoring by employing leave-one-out (LOO) cross-validation procedure to minimize overfitting to outlier outcome data
|
|
|
3
|
This pipeline works on R-2.5
|
S226953 |
Installed from zip
|
|
|
|
Look
describe it here
|
|
|
2
|
0
|
lamantiamaria@gmail.com |
Created on server
|
|
|
1
|
0
|
lamantiamaria@gmail.com |
Created on server
|
|
|
|
Lu.Getz.Miska.Nature.June.2005.mouse.lung.pipeline
Normal/tumor classifier and kNN prediction of mouse lung samples
|
|
|
1
|
Updated for R 2.5
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
Lu.Getz.Miska.Nature.June.2005.mouse.lung.pipeline2.0
Normal/tumor classifier and kNN prediction of mouse lung samples
|
|
|
1
|
Updated for R 2.5
|
edwin5588 |
Created on server
|
|
|
|
LUNAR
|
|
|
3
|
|
jpatrico |
Created on server
|
|
|
2
|
|
jpatrico |
Created on server
|
|
|
1
|
|
jpatrico |
Created on server
|
|
|
|
LUNAR_BINARY
|
|
|
2
|
|
jpatrico |
Created on server
|
|
|
1
|
|
jpatrico |
Created on server
|
|
|
|
LUSC
describe it here
|
|
|
1
|
0
|
ThanhNguyen |
Created on server
|
|
|
|
LUSC
describe it here
|
|
|
1
|
0
|
ThanhNguyen |
Created on server
|
|
|
|
M1_cluster
|
|
|
1
|
|
isabellestaco |
Created on server
|
|
|
|
M2_cluster
|
|
|
1
|
|
isabellestaco |
Created on server
|
|
|
|
M39715
|
|
|
1
|
|
spack |
Created on server
|
|
|
|
macro
|
|
|
1
|
|
apaoli |
Created on server
|
|
|
|
MAGEMLImportViewer
A visualizer to import data in MAGE-ML format into GenePattern
|
|
|
2
|
Fixes bug in determining if input file is in gzip format
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
MAGETABImportViewer
A visualizer to import data in MAGE-TAB format into GenePattern
|
|
|
2
|
Fixed bug with merging multiple data matrix files and also modified input parameters.
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
MakeHierarchicalClusterAndImage
|
|
|
1
|
|
alow |
Created on server
|
|
|
|
MapChipFeaturesGeneral
Change (map) the features (genes) of a dataset
|
|
|
3
|
Fixed a broken script reference
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
Mayo.MI
describe it here
|
|
|
1
|
0
|
tcimato |
Created on server
|
|
|
|
mbg2
|
|
|
1
|
|
RdvnAyaz |
Created on server
|
|
|
|
mbg421
|
|
|
1
|
|
RdvnAyaz |
Created on server
|
|
|
|
MedGen
|
|
|
4
|
|
lisaschneider0509 |
Created on server
|
|
|
3
|
|
lisaschneider0509 |
Created on server
|
|
|
2
|
|
lisaschneider0509 |
Created on server
|
|
|
1
|
|
lisaschneider0509 |
Created on server
|
|
|
|
MedGen
|
|
|
6
|
|
medgen |
Created on server
|
|
|
5
|
|
medgen |
Created on server
|
|
|
4
|
|
medgen |
Created on server
|
|
|
3
|
|
medgen |
Created on server
|
|
|
2
|
|
medgen |
Created on server
|
|
|
1
|
|
medgen |
Created on server
|
|
|
|
MedGen1
|
|
|
2
|
|
lisaschneider0509 |
Created on server
|
|
|
1
|
|
lisaschneider0509 |
Created on server
|
|
|
|
MedGen_Kallisto
|
|
|
1
|
|
lisaschneider0509 |
Created on server
|
|
|
|
MergeColumns
Merge datasets by column.
|
|
|
1
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
MergeFCSDataFiles
Merge multiple FCS data files into a single FCS datasets; includes multimple subsampling options.
|
|
|
1
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
MergeHTSeqCounts
Merges HTSeq read count data files into one file
|
|
|
1
|
Marked as production
|
tabor |
GenePattern production (new)
|
|
|
0.9
|
Marked as production
|
tabor |
GenePattern dev
|
|
|
0.7
|
Beta release with added feature of cls file creation and sample renaming
|
bhill@broadinstitute.org |
https://modulerepository.genepattern.org/gpModuleRepository//?env=dev
|
|
|
0.6
|
Beta release with added feature of cls file creation and sample renaming
|
bhill@broadinstitute.org |
Installed from zip
|
|
|
|
MergeRows
Merge datasets by row.
|
|
|
1
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
mesenchymal
describe it here
|
|
|
1
|
0
|
shamaineho |
Created on server
|
|
|
|
mesenchymal.pre
describe it here
|
|
|
1
|
0
|
carrano.anna@mayo.edu |
Created on server
|
|
|
|
MetageneProjection
Projects one or more data sets onto the metagene representation of another data set
|
|
|
1
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
MethylationCNVAnalysis
Methylation array preprocessing with the minfi R package and copy-number variation analysis with the conumee R package. Compatible with both 450k or EPIC array data.
|
|
|
4
|
Switch defaults to datasets from gpftp
|
ted |
GenePattern production (new)
|
|
|
3
|
Switch defaults to datasets from gpftp
|
ted |
GenePattern production (new)
|
|
|
2.4
|
geneslist optional
|
edjuaro |
GenePattern dev
|
|
|
2.3
|
Controls can also be EPIC 2019.
|
chapmano |
GenePattern production (new)
|
|
|
2.2
|
Update for EPIC 2019.
|
edjuaro |
GenePattern dev
|
|
|
1.0.0
|
|
ckmah |
Installed from zip
|
|
|
|
Microarray
|
|
|
3
|
|
tacazares |
Created on server
|
|
|
2
|
|
tacazares |
Created on server
|
|
|
1
|
|
tacazares |
Created on server
|
|
|
|
mihriban
describe it here
|
|
|
1
|
0
|
aydogan |
Created on server
|
|
|
|
mihriban
describe it here
|
|
|
2
|
0
|
aydogan |
Created on server
|
|
|
1
|
0
|
aydogan |
Created on server
|
|
|
|
mihriban
describe it here
|
|
|
1
|
0
|
aydogan |
Created on server
|
|
|
|
MINDY
Runs the MINDY algorithm for inferring genes that modulate the activity of a transcription factor at post-transcriptional levels
|
|
|
2
|
Fixed parsing of optional parameter dpi transcription factor list on command line
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
MINDYViewer
Visualizes the results of MINDY
|
|
|
1
|
Visualizes the results of MINDY
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
mirna.analysis
describe it here
|
|
|
2
|
0
|
kpagacz |
Created on server
|
|
|
1
|
0
|
kpagacz |
Created on server
|
|
|
|
monse
describe it here
|
|
|
1
|
0
|
monser9610 |
Created on server
|
|
|
|
monse
describe it here
|
|
|
1
|
0
|
monser9610 |
Created on server
|
|
|
|
monse
describe it here
|
|
|
1
|
0
|
monser9610 |
Created on server
|
|
|
|
MouseLiver
|
|
|
1
|
|
yiwenh |
Created on server
|
|
|
|
MouseLiver
|
|
|
1
|
|
yiwenh |
Created on server
|
|
|
|
MS_gene.enrichment
|
|
|
1
|
|
Jinxi |
Created on server
|
|
|
|
multi.gsea
|
|
|
3
|
|
stonilee |
Created on server
|
|
|
2
|
|
stonilee |
Created on server
|
|
|
1
|
|
stonilee |
Created on server
|
|
|
|
Multiple.ssGSEA
|
|
|
3
|
|
thk1 |
Created on server
|
|
|
2
|
|
thk1 |
Created on server
|
|
|
1
|
|
thk1 |
Created on server
|
|
|
|
Multiple_ssGSEA_ROC
Simple_ssGSEA_ROC
|
|
|
11
|
|
TaeHoon5314 |
Created on server
|
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10
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TaeHoon5314 |
Created on server
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9
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TaeHoon5314 |
Created on server
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8
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TaeHoon5314 |
Created on server
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7
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TaeHoon5314 |
Created on server
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6
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TaeHoon5314 |
Created on server
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5
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TaeHoon5314 |
Created on server
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4
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TaeHoon5314 |
Created on server
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3
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TaeHoon5314 |
Created on server
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2
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TaeHoon5314 |
Created on server
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1
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TaeHoon5314 |
Created on server
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Multiple_ssGSEA_ROC
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3
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thk1 |
Created on server
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2
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thk1 |
Created on server
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1
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thk1 |
Created on server
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MultiplotStudio
Scatterplot visualization tool for analyzing differential gene expression.
|
|
|
1.5.62
|
Completely rewritten and vastly improved replacement for Multiplot
|
bhill@broadinstitute.org |
Installed from zip
|
|
|
|
MutPanning
MutPanning identifies driver genes based on their abundance of nonsynonymous mutations and their increased number of mutations in unusual nucleotide contexts that deviate from the background mutational process.
|
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2
|
Initial Release
|
bhill@broadinstitute.org |
Installed from zip
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MutSig
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1
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SwethaRaj |
Created on server
|
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MutSig_01
describe it here
|
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2
|
0
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lilianboll |
Created on server
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1
|
0
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lilianboll |
Created on server
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mutsig_lt1
mutsig
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1
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|
gracejoo@skku.edu |
Created on server
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mutsig_ref
|
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1
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|
gracejoo@skku.edu |
Created on server
|
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MutSigCV
Identifies genes that are significantly mutated in cancer genomes, using a model with mutational covariates.
|
|
|
1.3
|
Moved gp_MutSigCV executable into the 'genepattern/docker-mutsigcv:0.2' docker image
|
pcarr@broadinstitute.org |
https://modulerepository.genepattern.org/gpModuleRepository//?env=dev
|
|
|
1.3.5
|
updated taskType
|
bhill@broadinstitute.org |
GenePattern production (new)
|
|
|
1.3.4
|
Copied gp_MutSigCV to docker image
|
pcarr@broadinstitute.org |
Installed from zip
|
|
|
1.2
|
Remove python dependency, use 'Matlab-2013a-MCR' environment and directly invoke the gp_MutSigCV executable
|
pcarr@broadinstitute.org |
https://modulerepository.genepattern.org/gpModuleRepository//?env=dev
|
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|
my.bowite.indexer
describe it here
|
|
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2
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0
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csusm |
Created on server
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1
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0
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csusm |
Created on server
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MycMut_Exp
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1
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lysis_2_kill |
Created on server
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MyComparativeMarkerSelection
Identify differentially expressed genes
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2
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0
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ValentinaJG |
Created on server
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1
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0
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ValentinaJG |
Created on server
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MyComparativeMarkerSelection
Identify differentially expressed genes
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4
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Abrilmercado |
Created on server
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3
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Abrilmercado |
Created on server
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2
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0
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Abrilmercado |
Created on server
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1
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0
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Abrilmercado |
Created on server
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MyComparativeMarkerSelection
identify differentially expressed genes
|
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3
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amirferry |
Created on server
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2
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0
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amirferry |
Created on server
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1
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0
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amirferry |
Created on server
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MyComparativeMarkerSelection
Identify differentially expressed genes
|
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3
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amirferry |
Created on server
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2
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0
|
amirferry |
Created on server
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1
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0
|
amirferry |
Created on server
|
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MyComparativeMarkerSelection
describe it here
|
|
|
4
|
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Mgrinwald |
Created on server
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3
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Mgrinwald |
Created on server
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2
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0
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Mgrinwald |
Created on server
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1
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0
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Mgrinwald |
Created on server
|
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MyComparativeMarkerSelection
describe it here
|
|
|
3
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christoftaxis |
Created on server
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2
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0
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christoftaxis |
Created on server
|
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1
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0
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christoftaxis |
Created on server
|
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MyComparativeMarkerSelection
identify differentially expressed genes
|
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|
4
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Lucas Huang |
Created on server
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3
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Lucas Huang |
Created on server
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2
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0
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Lucas Huang |
Created on server
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1
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0
|
Lucas Huang |
Created on server
|
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MyComparativeMarkerSelection
ID differentially expressed genes
|
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1
|
|
saipra003@gmail.com |
Created on server
|
|
|
|
MyComparativeMarkerSelection
describe it here
|
|
|
3
|
|
firoz |
Created on server
|
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2
|
0
|
firoz |
Created on server
|
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1
|
0
|
firoz |
Created on server
|
|
|
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MyComparativeMarkerSelection
Identify differentially expressed genes
|
|
|
4
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ch211493 |
Created on server
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3
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ch211493 |
Created on server
|
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2
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0
|
ch211493 |
Created on server
|
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1
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0
|
ch211493 |
Created on server
|
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Mycomparativemarkerselection
describe it here
|
|
|
2
|
0
|
acelyaavci |
Created on server
|
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1
|
0
|
acelyaavci |
Created on server
|
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mycomparativemarkerselection
describe it here
|
|
|
2
|
0
|
acelyaavci |
Created on server
|
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1
|
0
|
acelyaavci |
Created on server
|
|
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MyComparativeMarkerSelection
Identify differential gene expression
|
|
|
3
|
0
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jacquelinemartin |
Created on server
|
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2
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0
|
jacquelinemartin |
Created on server
|
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1
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0
|
jacquelinemartin |
Created on server
|
|
|
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MyComparativeMarkerSelection
describe it here
|
|
|
1
|
0
|
jacquelinemartin |
Created on server
|
|
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MyComparativeMarkerSelection
DEG aml
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4
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sdeota |
Created on server
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3
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sdeota |
Created on server
|
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2
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0
|
sdeota |
Created on server
|
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1
|
0
|
sdeota |
Created on server
|
|
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MyComparativeMarkerSelection
describe it here
|
|
|
6
|
|
rnm53 |
Created on server
|
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5
|
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rnm53 |
Created on server
|
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4
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rnm53 |
Created on server
|
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3
|
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rnm53 |
Created on server
|
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2
|
0
|
rnm53 |
Created on server
|
|
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1
|
0
|
rnm53 |
Created on server
|
|
|
|
MyComparativeMarkerSelection
describe it here
|
|
|
2
|
0
|
lalevesque95 |
Created on server
|
|
|
1
|
0
|
lalevesque95 |
Created on server
|
|
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MyComparativeMarkerSelection
expressed gene
|
|
|
4
|
|
nayoung828 |
Created on server
|
|
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3
|
|
nayoung828 |
Created on server
|
|
|
2
|
0
|
nayoung828 |
Created on server
|
|
|
1
|
0
|
nayoung828 |
Created on server
|
|
|
|
MyComparativeMarkerSelection
identify differentially expressed genes
|
|
|
3
|
0
|
ssridhar |
Created on server
|
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|
2
|
0
|
ssridhar |
Created on server
|
|
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1
|
0
|
ssridhar |
Created on server
|
|
|
|
MyCompartiveMarkerSelection
Identify differentially expressed genes
|
|
|
4
|
|
jacquelinemartin |
Created on server
|
|
|
3
|
|
jacquelinemartin |
Created on server
|
|
|
2
|
0
|
jacquelinemartin |
Created on server
|
|
|
1
|
0
|
jacquelinemartin |
Created on server
|
|
|
|
MyCompartiveMarkerSelection
identifying differentially expressed genes
|
|
|
3
|
|
khalil.z |
Created on server
|
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2
|
0
|
khalil.z |
Created on server
|
|
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1
|
0
|
khalil.z |
Created on server
|
|
|
|
MyComprativeMarkerSelection
Identify differentially expressed genes
|
|
|
6
|
|
Abrilmercado |
Created on server
|
|
|
5
|
|
Abrilmercado |
Created on server
|
|
|
4
|
|
Abrilmercado |
Created on server
|
|
|
3
|
|
Abrilmercado |
Created on server
|
|
|
2
|
0
|
Abrilmercado |
Created on server
|
|
|
1
|
0
|
Abrilmercado |
Created on server
|
|
|
|
MyogenicDifferentiation
|
|
|
1
|
|
busrayi |
Created on server
|
|
|
|
MyPipelien
describe it here
|
|
|
1
|
0
|
firoz |
Created on server
|
|
|
|
myPipeline
|
|
|
1
|
|
fravitali |
Created on server
|
|
|
|
mzXMLToCsv
Converts a mzXML file to a zip of csv files
|
|
|
1
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
N22
describe it here
|
|
|
1
|
0
|
ymavura |
Created on server
|
|
|
|
NanoStringNormalizer
|
|
|
1
|
|
ecrouchet@unistra.fr |
Created on server
|
|
|
|
NearestTemplatePrediction
Nearest neighbor prediction based on a list of marker genes
|
|
|
6
|
Updated to use R-3.1 and added HTML documentation.
|
ted |
GenePattern production (new)
|
|
|
4
|
Updated to use R-3.1 and added HTML documentation.
|
pcarr@broadinstitute.org |
GParc (GenePattern Archive)
|
|
|
|
NivoTad.Supervised.GSEA
|
|
|
1
|
|
Jefferson |
Created on server
|
|
|
|
NMF
describe it here
|
|
|
1
|
0
|
monser9610 |
Created on server
|
|
|
|
NMF
Non-negative Matrix Factorization
|
|
|
2
|
Annotated for GP 1.4
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
2.1
|
Annotated for GP 1.4
|
tabor |
GenePattern dev
|
|
|
|
NMFClustering
GPU-backed implementation of non-negative Matrix Factorization (NMF) Consensus Clustering.
|
|
|
7
|
Using mini-batch k-means for clustering
|
ted |
Installed from zip
|
|
|
|
NMFConsensus
Non-negative Matrix Factorization (NMF) Consensus Clustering
|
|
|
5
|
Added output files to manifest. Doc edits.
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
no1
describe it here
|
|
|
1
|
0
|
amaretto-team |
Created on server
|
|
|
|
No_exo_1_R1.fastq.gz
describe it here
|
|
|
1
|
0
|
thepreztonlee |
Created on server
|
|
|
|
Normalizacin
describe it here
|
|
|
1
|
0
|
nashe_li |
Created on server
|
|
|
|
Normalization.Nanostring
|
|
|
2
|
|
nevena.slovic@etu.unistra.fr |
Created on server
|
|
|
1
|
|
nevena.slovic@etu.unistra.fr |
Created on server
|
|
|
|
normalizeRNAseq
|
|
|
2
|
|
edjuaro |
Created on server
|
|
|
1
|
|
edjuaro |
Created on server
|
|
|
|
nur.demirci
describe it here
|
|
|
1
|
0
|
nurdemirci |
Created on server
|
|
|
|
Nur.DEMRC
describe it here
|
|
|
2
|
0
|
nurdemirci |
Created on server
|
|
|
1
|
0
|
nurdemirci |
Created on server
|
|
|
|
One
describe it here
|
|
|
2
|
0
|
Amrutesh |
Created on server
|
|
|
1
|
0
|
Amrutesh |
Created on server
|
|
|
|
oo
describe it here
|
|
|
1
|
0
|
wklove |
Created on server
|
|
|
|
oooo
describe it here
|
|
|
1
|
0
|
SENTHIL |
Created on server
|
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|
|
OpenCRAVAT
<img src="https://opencravat.org/images/OpenCRAVAT_Logo-0-sm.png" width=50px alt="img"/>OpenCRAVAT performs genomic variant interpretation including variant impact, annotation, and scoring.
|
|
|
1
|
inital release
|
bhill@broadinstitute.org |
GenePattern production (new)
|
|
|
1.3
|
inital release
|
ted |
Installed from zip
|
|
|
1.1
|
inital release
|
ted |
Installed from zip
|
|
|
|
OutSplice
OutSplice is a package that compares alternative splicing events between tumor and normal samples. This package is specifically designed for analyzing the gene and junction information from RNA sequencing data provided by the user, or from the TCGA. This package generates a matrix of splicing outliers, which are junctions that are either significantly over or under-expressed compared to a control sample. OutSplice further designates observed outliers as skipping, insertion, or deletion events. Overall, OutSplice is novel in that it determines differential splicing burdens between tumors and normal samples and characterizes the nature of splicing outliers.
|
|
|
3
|
Remove genome, txdb and annotation parameters, leaving only the presets
|
ted |
GenePattern production (new)
|
|
|
2
|
Remove genome, txdb and annotation parameters, leaving only the presets
|
ted |
GenePattern production (new)
|
|
|
1
|
Remove genome, txdb and annotation parameters, leaving only the presets
|
ted |
GenePattern production (new)
|
|
|
|
OutSplice.plotJunctions
Using the result file from OutSplice, OutSplice.plotJunctions creates bar and waterfall plots of junction expression in both the tumor and normal samples.
|
|
|
3
|
Initial Revision.
|
ted |
GenePattern production (new)
|
|
|
2
|
Initial Revision.
|
ted |
GenePattern production (new)
|
|
|
1
|
Initial Revision.
|
ted |
GenePattern production (new)
|
|
|
|
Ovarian_EMT
describe it here
|
|
|
14
|
|
lalevesque95 |
Created on server
|
|
|
13
|
|
lalevesque95 |
Created on server
|
|
|
13.3
|
|
lalevesque95 |
Created on server
|
|
|
13.2
|
|
lalevesque95 |
Created on server
|
|
|
13.2.3
|
|
lalevesque95 |
Created on server
|
|
|
13.2.2
|
|
lalevesque95 |
Created on server
|
|
|
13.2.1
|
|
lalevesque95 |
Created on server
|
|
|
13.1
|
|
lalevesque95 |
Created on server
|
|
|
12
|
|
lalevesque95 |
Created on server
|
|
|
11
|
|
lalevesque95 |
Created on server
|
|
|
10
|
|
lalevesque95 |
Created on server
|
|
|
9
|
|
lalevesque95 |
Created on server
|
|
|
8
|
|
lalevesque95 |
Created on server
|
|
|
7
|
|
lalevesque95 |
Created on server
|
|
|
6
|
|
lalevesque95 |
Created on server
|
|
|
5
|
|
lalevesque95 |
Created on server
|
|
|
4
|
|
lalevesque95 |
Created on server
|
|
|
3
|
|
lalevesque95 |
Created on server
|
|
|
2
|
0
|
lalevesque95 |
Created on server
|
|
|
1
|
0
|
lalevesque95 |
Created on server
|
|
|
|
PAAD_CNV
|
|
|
1
|
|
chuting |
Created on server
|
|
|
|
PAAD_CNV1
|
|
|
2
|
|
chuting |
Created on server
|
|
|
1
|
|
chuting |
Created on server
|
|
|
|
PCA
Principal Component Analysis (adapted from MeV, http://www.tm4.org/m)
|
|
|
4
|
Updated documentation
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
4.2
|
Updated documentation
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
4.1
|
Updated documentation
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
|
pca
describe it here
|
|
|
1
|
0
|
trandoanduyhai |
Created on server
|
|
|
|
PCAViewer
Principal Component Analysis Visualizer (adapted from MeV, http://www.tigr.org/software/tm4/mev.html)
|
|
|
6
|
Fixed bug with 3D plot with legend not properly saved on non-Windows machines
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
PclToGct
Convert Stanford preclustering file (.pcl) to .gct
|
|
|
1
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
PCNSL_MutSigCV
|
|
|
2
|
|
xeyu17@fudan.edu.cn |
Created on server
|
|
|
1
|
|
xeyu17@fudan.edu.cn |
Created on server
|
|
|
|
PD1
|
|
|
1
|
|
studyong |
Created on server
|
|
|
|
PD2
|
|
|
1
|
|
studyong |
Created on server
|
|
|
|
PDL1lung
|
|
|
1
|
|
studyong |
Created on server
|
|
|
|
Peaks
Determine peaks in the spectrum using a series of digital filters.
|
|
|
2
|
Updated for R 2.5
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
philip
describe it here
|
|
|
2
|
0
|
landa |
Created on server
|
|
|
1
|
0
|
landa |
Created on server
|
|
|
|
Picard.AddOrReplaceReadGroups
Replaces all read groups in the input file with a new read group and assigns all reads to this read group in the output
|
|
|
3
|
Read Group ID is now a required Parameter.
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
Picard.BamToSam
Converts a BAM file to a SAM file
|
|
|
2
|
Renamed from BamToSam to Picard.BamToSam
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
Picard.CreateSequenceDictionary
Reads FASTA or FASTA.GZ files containing reference sequences, and writes them as a SAM file containing a sequence dictionary
|
|
|
1
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
Picard.FastqToSam
Extracts read sequences and qualities from the input fastq file and writes them into the output file in unaligned SAM or BAM format
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2
|
Renamed from FastqToSam to Picard.FastqToSam
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pcarr@broadinstitute.org |
GenePattern production (new)
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Picard.MarkDuplicates
Examines aligned records in the supplied SAM or BAM file to locate duplicate reads.
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2
|
Added sorting collection size ratio parameter and modified to print warning message about failed file delete attempts to stdout
|
pcarr@broadinstitute.org |
GenePattern production (new)
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Picard.ReorderSam
Reorders a SAM file or a BAM file to match contig ordering in a provided reference file
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1
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pcarr@broadinstitute.org |
GenePattern production (new)
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Picard.SamToBam
Converts a SAM file to a BAM file
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2
|
Renamed from SamToBam to Picard.SamToBam
|
pcarr@broadinstitute.org |
GenePattern production (new)
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Picard.SamToFastq
Convert SAM or BAM files to FASTQ format
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3
|
Fixed issue with choice parameters not appearing as drop downs
|
pcarr@broadinstitute.org |
GenePattern production (new)
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Picard.SortSam
Sorts a SAM or BAM file in a specified order
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4
|
Renamed from SortSam to Picard.SortSam
|
pcarr@broadinstitute.org |
GenePattern production (new)
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pip
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1
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Angelica461 |
Created on server
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pip
describe it here
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1
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0
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applehur |
Created on server
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PIPE1
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1
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chuting |
Created on server
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Pipe_MutSigCV
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1
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sguib |
Created on server
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Pipeline
describe it here
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1
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0
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aster1217@gmail.com |
Created on server
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Pipeline
describe it here
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2
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0
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yuduoduo |
Created on server
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1
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0
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yuduoduo |
Created on server
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PIPELINE
describe it here
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1
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0
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monser9610 |
Created on server
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Pipeline
describe it here
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1
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0
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Nour1 |
Created on server
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Pipeline
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1
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sevvaldik |
Created on server
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Pipeline
describe it here
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1
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0
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Nour1 |
Created on server
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Pipeline.0421
describe it here
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1
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0
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keina.0328@gmail.com |
Created on server
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Pipeline.0522
describe it here
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1
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0
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keina.0328@gmail.com |
Created on server
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Pipeline.07112020
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4
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mauro campanella |
Created on server
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3
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mauro campanella |
Created on server
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2
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mauro campanella |
Created on server
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1
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mauro campanella |
Created on server
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Pipeline.1
describe it here
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1
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0
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ValentinaJG |
Created on server
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Pipeline.1
describe it here
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1
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0
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Abrilmercado |
Created on server
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Pipeline.1
describe it here
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1
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0
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khushbhullar |
Created on server
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Pipeline.1
describe it here
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1
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0
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ivanz@vin.bg.ac.rs |
Created on server
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Pipeline.1
describe it here
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1
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0
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MoonSun |
Created on server
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Pipeline.1
describe it here
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1
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0
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kuelp |
Created on server
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Pipeline.1
describe it here
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1
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0
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ychmax8@gmail.com |
Created on server
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Pipeline.1
describe it here
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1
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0
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Shakira |
Created on server
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Pipeline.1.comparative.marker.selection.
describe it here
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2
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0
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kathyhan98 |
Created on server
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1
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0
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kathyhan98 |
Created on server
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Pipeline.1.kmeansclustering
describe it here
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2
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0
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kathyhan98 |
Created on server
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1
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0
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kathyhan98 |
Created on server
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Pipeline.11
describe it here
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1
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0
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YuanLin |
Created on server
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Pipeline.11
describe it here
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1
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0
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Drhai |
Created on server
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Pipeline.123
describe it here
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1
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0
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b1951951 |
Created on server
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Pipeline.1st
describe it here
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1
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0
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jooyong0308@gmail.com |
Created on server
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Pipeline.2
describe it here
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1
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0
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lbaert |
Created on server
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Pipeline.2
describe it here
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1
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0
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mahaitao18580092262 |
Created on server
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Pipeline.2.comparative.marker.selection
identify DE genes
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5
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kathyhan98 |
Created on server
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4
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kathyhan98 |
Created on server
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3
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kathyhan98 |
Created on server
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2
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0
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kathyhan98 |
Created on server
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1
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0
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kathyhan98 |
Created on server
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Pipeline.2.kmeansclustering.
describe it here
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3
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0
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kathyhan98 |
Created on server
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2
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0
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kathyhan98 |
Created on server
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1
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0
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kathyhan98 |
Created on server
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Pipeline.20190712DNM2RNAseq
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1
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yaling.wu |
Created on server
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Pipeline.2D3D.compare
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2
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cjk31714 |
Created on server
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1
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cjk31714 |
Created on server
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Pipeline.33
describe it here
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1
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0
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apacis |
Created on server
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Pipeline.4
describe it here
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1
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0
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dolphin |
Created on server
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Pipeline.48sample_chishao
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1
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Daisy Dai |
Created on server
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Pipeline.55
describe it here
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1
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0
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yitao |
Created on server
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Pipeline.72h_znf
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1
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lysk3490 |
Created on server
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Pipeline.88
describe it here
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1
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0
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jessie61886@gmail.com |
Created on server
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Pipeline.92.1.FR92.1.DMSO.Onken
describe it here
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1
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0
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eanderson34 |
Created on server
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Pipeline.all_thresholded.by_genes.txt.
describe it here
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2
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0
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guest_96206 |
Created on server
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1
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0
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guest_96206 |
Created on server
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Pipeline.for.QC.and.normalisation.of.EMEXP3583
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1
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Shakira |
Created on server
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Pipeline.MyComparativeMarkerSelection
Identify differentially expressed genes
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3
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ch211493 |
Created on server
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2
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0
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ch211493 |
Created on server
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1
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0
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ch211493 |
Created on server
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Pipeline.MyComparativeMarkerSelection
identify differentially expressed genes
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4
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s6swchan |
Created on server
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3
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s6swchan |
Created on server
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2
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0
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s6swchan |
Created on server
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1
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0
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s6swchan |
Created on server
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pipeline.tutorial
describe it here
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1
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0
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zhanglim3 |
Created on server
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pipeline_eserc
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1
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Alberto_Gualtieri_1993 |
Created on server
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pipeline_rep
describe it here
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3
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0
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sciencekey |
Created on server
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2
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0
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sciencekey |
Created on server
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1
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0
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sciencekey |
Created on server
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Pipeline_test_EM
RNA Seq 2 groups
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1
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v1
|
etienne.moussay@lih.lu |
Created on server
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PipelineKNN_test
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1
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alsawao |
Created on server
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pipline_esercitazione
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1
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Alberto_Gualtieri_1993 |
Created on server
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PippaLine
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1
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isaia |
Created on server
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plot
describe it here
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1
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0
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lisdasuteja |
Created on server
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PlotPeaks
Plot peaks
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2
|
Updated for R 2.5
|
pcarr@broadinstitute.org |
GenePattern production (new)
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PlvCtrl6308
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1
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|
singhuh00 |
Created on server
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PNGNMFConsensus
Non-negative Matrix Factorization (NMF) Consensus Clustering
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2
|
convert pdf to png
|
ted |
Created on server
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1
|
Added output files to manifest. Doc edits.
|
ted |
Created on server
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polyau_preleuk_ssgsea_test
describe it here
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1
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0
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samuel1 |
Created on server
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polyau_ssgsea_viz_testing
describe it here
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1
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0
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samuel1 |
Created on server
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pp
describe it here
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1
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0
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coco06 |
Created on server
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pptm
describe it here
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1
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0
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jgriffin567 |
Created on server
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practice1
describe it here
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1
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0
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kedar |
Created on server
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PredictionResultsViewer
Visualizes prediction results in JavaScript
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4.11
|
Bug fix for S3 files
|
tabor |
GenePattern production (new)
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4.10
|
JavaScript implementation of PredictionResultsViewer
|
bhill@broadinstitute.org |
https://modulerepository.genepattern.org/gpModuleRepository//?env=dev
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4.9
|
JavaScript implementation of PredictionResultsViewer
|
bhill@broadinstitute.org |
GenePattern production (new)
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1
|
Includes interactive plot of prediction results
|
pcarr@broadinstitute.org |
GenePattern production (new)
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Preprocess_tutorial
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1
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|
alsawao |
Created on server
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PreprocessDataset
Performs several preprocessing steps on a res, gct, or odf input file
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5
|
convert over to html doc
|
pcarr@broadinstitute.org |
Installed from zip
|
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5.1
|
Bug fix for optional 'threshold.for.removing.rows' and 'number.of.columns.above.threshold' module params
|
ted |
GenePattern production (new)
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2
|
Added additional filtering options
|
pcarr@broadinstitute.org |
GenePattern production (new)
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preprocessed.gct
describe it here
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1
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0
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96Gerar |
Created on server
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PreprocessVelocityTranscriptome
Extract transcript and intron sequences from the genome sequence using the eisaR package in order to quantify both intronic (unprocessed) and exonic (processed) RNA abundances in each cell with alevin.<br>A necessary preprocessing step to enable RNA velocity analysis.
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1
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initial release
|
bhill@broadinstitute.org |
GenePattern production (new)
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PreviewFCS
Allows viewing of structural metadata, parameters, and descriptive statistics from a Flow Cytometry Standard (FCS) data file
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2
|
Fix for parsing empty keyword values
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pcarr@broadinstitute.org |
GenePattern production (new)
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PrivateCloud
test of permissions
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1
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ted |
Created on server
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process
describe it here
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2
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0
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HUANGSHUAI |
Created on server
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1
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0
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HUANGSHUAI |
Created on server
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Processing
describe it here
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1
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0
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smgxopk |
Created on server
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ProstateMRSamp1
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1
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trostels |
Created on server
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ProteoArray
LC-MS proteomic data processing module
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1
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pcarr@broadinstitute.org |
GenePattern production (new)
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proteoGSEA_Ant_Rome
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1
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ferjmnz |
Created on server
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ProteomicsAnalysis
Runs the proteomics analysis on the set of input spectra
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2
|
Updated for R 2.5
|
pcarr@broadinstitute.org |
GenePattern production (new)
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prova
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1
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AngelicaR |
Created on server
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prova
describe it here
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1
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0
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AFALANGA |
Created on server
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Prova
describe it here
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1
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0
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g.armani |
Created on server
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prova
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1
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debora_dallera |
Created on server
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prova.2
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2
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mauro campanella |
Created on server
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1
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mauro campanella |
Created on server
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Prova1
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1
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debora_dallera |
Created on server
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Prova1
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6
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Mattia_gp2 |
Created on server
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5
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Mattia_gp2 |
Created on server
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4
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Mattia_gp2 |
Created on server
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3
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Mattia_gp2 |
Created on server
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2
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Mattia_gp2 |
Created on server
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1
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Mattia_gp2 |
Created on server
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Prova1
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1
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Giuseppe.serio01 |
Created on server
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prova_bioinformatica
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1
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valentina1 |
Created on server
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prova_corso_bioinf_AT
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3
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Alicesalvadeo |
Created on server
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2
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Alicesalvadeo |
Created on server
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1
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Alicesalvadeo |
Created on server
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prova_corsoBioinformatica
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2
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Mattia_gp2 |
Created on server
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1
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Mattia_gp2 |
Created on server
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PTM_SEA
PTM-SEA for use with PTMsigDB
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4
|
Initial Version to accompany PTM-SEA manuscript
|
pcarr@broadinstitute.org |
Installed from zip
|
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2
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0
|
pcarr@broadinstitute.org |
Created on server
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1
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0
|
pcarr@broadinstitute.org |
Created on server
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PTMSEA.Pipeline.FMA
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1
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fahsan |
Created on server
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PTMSEA.try
describe it here
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1
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0
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gramirez |
Created on server
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pvec.paper
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1
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fkipper |
Created on server
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pvec_npc.vs.pvec
describe it here
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1
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0
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fkipper |
Created on server
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PyCoGAPS
Coordinated Gene Activity in Pattern Sets (CoGAPS) implements a Bayesian MCMC matrix factorization algorithm, GAPS, and links it to gene set statistic methods to infer biological process activity. It can be used to perform sparse matrix factorization on any data, and when this data represents biomolecules, to do gene set analysis. This package, PyCoGAPS, presents a unified Python interface, with a parallel, efficient underlying implementation.
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4
|
Updated parameter descriptions for max gibbs A and P
|
ted |
GenePattern production (new)
|
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3
|
Updated parameter descriptions for max gibbs A and P
|
ted |
GenePattern production (new)
|
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2
|
Updated parameter descriptions for max gibbs A and P
|
ted |
GenePattern production (new)
|
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|
1
|
Updated parameter descriptions for max gibbs A and P
|
ted |
GenePattern production (new)
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|
q
describe it here
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1
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0
|
MartaRojas |
Created on server
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qPCR_heatmap_secscreen
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1
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cbudjan |
Created on server
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qupathtofcsPipeline
qupath
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1
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gabrielascui |
Created on server
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r
describe it here
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1
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0
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kimmcl860 |
Created on server
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raanvi
describe it here
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1
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0
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raanvi |
Created on server
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ran.seq
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3
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bioraghu |
Created on server
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2
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bioraghu |
Created on server
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1
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bioraghu |
Created on server
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RandomForest
Performs random forest classification on data and class files (cross-validation or test-train prediction), outputting a prediction results file.
|
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4
|
Module filename bug fixes
|
edwin5588 |
GenePattern production (new)
|
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2
|
Version 2, includes confidence scores, feature importance, and model in/output
|
edwin5588 |
GenePattern production (new)
|
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|
1
|
Initial beta version (equivalent to Dev 1.0)
|
edwin5588 |
GenePattern production (new)
|
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|
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RankNormalize
Normalize the rows in a data set by rank
|
|
|
1.10
|
Updated to make use of the R package installer and add HTML documentation.
|
edwin5588 |
GenePattern dev
|
|
|
|
Read_group_trackingToGct
[**Beta Release** Contact gp-help with any issues. Check stdout.txt and stderr.txt for errors] Converts a Cufflinks read_group_tracking file into GCT format
|
|
|
0.15
|
Updated to accept a mapping file to convert tracking IDs to gene names.
|
pcarr@broadinstitute.org |
GenePattern beta
|
|
|
|
reg
describe it here
|
|
|
1
|
0
|
Rezwan |
Created on server
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REMBRANDT.pipeline
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3
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svdvoort |
Created on server
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2
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|
svdvoort |
Created on server
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1
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|
svdvoort |
Created on server
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RemoveMissingValues
Removes features and/or samples containing missing (NA) values
|
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1
|
Public Release
|
pcarr@broadinstitute.org |
GenePattern production (new)
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|
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RemoveSaturatedFCSEvents
Remove saturated events from an FCS data file
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1
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
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|
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RenameFile
Creates a result file with the contents of the input but with a new name. Where possible, this is done without copying the file but instead by simply making a link. While it is possible to run this with a submitted file, the common use will be to change the name of a result file or a previously uploaded file. Note that the original file will still be present in its original location.
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1
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|
pcarr@broadinstitute.org |
GenePattern production (new)
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ReorderByClass
Reorder the samples in an expression dataset and class file by class
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3
|
Fixed default value for class file output name
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
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report
describe it here
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1
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0
|
aru2001 |
Created on server
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results
describe it here
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1
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0
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sdh1621 |
Created on server
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rf
describe it here
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1
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0
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ameetmishra |
Created on server
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RNA.Prdm12
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1
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tkokotovic |
Created on server
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RNA.seq.analysis.test.2.tuxedo_new
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1
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jdyee |
Created on server
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rna.seq.KI.vs.WT
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1
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bioraghu |
Created on server
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RNA_EX
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2
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osamasweef |
Created on server
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1
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osamasweef |
Created on server
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RNA_exp
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1
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jmargari |
Created on server
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RNA_exp
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1
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|
Takeshi Masuda |
Created on server
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RNA_exp
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1
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jbzhang |
Created on server
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RNA_seq
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3
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byuen_pactpharma |
Created on server
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2
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byuen_pactpharma |
Created on server
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1
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byuen_pactpharma |
Created on server
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RNA_seq
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1
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seisen27 |
Created on server
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RNA_Seq
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1
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seisen27 |
Created on server
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rna_seq
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3
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|
scientistbill |
Created on server
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2
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scientistbill |
Created on server
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1
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scientistbill |
Created on server
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RNAExp
|
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1
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aximinies |
Created on server
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RNAexp_PVL20200402
RNA seq pipeline for bulk rna
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1
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desai.krisha |
Created on server
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RNAseq
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1
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|
wmr23 |
Created on server
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rnaseq
describe it here
|
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2
|
0
|
ddaizi |
Created on server
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1
|
0
|
ddaizi |
Created on server
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RNAseq
|
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1
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|
xiaohua |
Created on server
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rnaseq
describe it here
|
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4
|
0
|
mmurugesan@coh.org |
Created on server
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3
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0
|
mmurugesan@coh.org |
Created on server
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2
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0
|
mmurugesan@coh.org |
Created on server
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1
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0
|
mmurugesan@coh.org |
Created on server
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RNAseq
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1
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|
jbzhang |
Created on server
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RNASeq
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5
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VeraK |
Created on server
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4
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VeraK |
Created on server
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3
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VeraK |
Created on server
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2
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VeraK |
Created on server
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1
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VeraK |
Created on server
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RNAseq.analysis.test.run
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1
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jdyee |
Created on server
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RNAseq.GSEA
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1
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pem20bf |
Created on server
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RNAseq.pipeline.v1
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3
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|
userlee7655-2 |
Created on server
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2
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|
userlee7655-2 |
Created on server
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1
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|
userlee7655-2 |
Created on server
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RNAseq.sms4
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1
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Samii8 |
Created on server
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RNASeq.TCGA
|
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1
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|
jsussman |
Created on server
|
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RNAseq_corso_bioinf
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2
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|
Matteo |
Created on server
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1
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|
Matteo |
Created on server
|
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RNAseq_DESeq2
RNA seq DESeq2
|
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12
|
|
etienne.moussay@lih.lu |
Created on server
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11
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|
etienne.moussay@lih.lu |
Created on server
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10
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|
etienne.moussay@lih.lu |
Created on server
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9
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|
etienne.moussay@lih.lu |
Created on server
|
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8
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|
etienne.moussay@lih.lu |
Created on server
|
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7
|
|
etienne.moussay@lih.lu |
Created on server
|
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6
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|
etienne.moussay@lih.lu |
Created on server
|
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5
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|
etienne.moussay@lih.lu |
Created on server
|
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4
|
|
etienne.moussay@lih.lu |
Created on server
|
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1.1
|
v1
|
etienne.moussay@lih.lu |
Created on server
|
|
|
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RNAseq_exp
|
|
|
1
|
|
xiaohua |
Created on server
|
|
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RNAseqc
|
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3
|
|
bgfritz1 |
Created on server
|
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2
|
|
bgfritz1 |
Created on server
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1
|
|
bgfritz1 |
Created on server
|
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|
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RNASeQC
Calculates metrics on aligned RNA-seq data.
|
|
|
2
|
Renamed from RNAseqMetrics
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
2.15
|
Beta Release: Updated with RNASeQC.jar build 8.7.13. Currently outputs INFO and WARNING to stdout
|
pcarr@broadinstitute.org |
GenePattern beta
|
|
|
|
rtgg
describe it here
|
|
|
1
|
0
|
JavierRobles272 |
Created on server
|
|
|
|
SageKda2Cys
Takes a zip of KeyDriverAnalysis output files and formats them as a cytoscape .cys session file
|
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|
6
|
|
tabor |
GenePattern dev
|
|
|
|
Salmon.Alevin.Quant
Quantification and analysis of 3' tagged-end single-cell sequencing data using Salmon's Alevin (v1.5.2) function.<br>
See: <a href="https://salmon.readthedocs.io/en/latest/alevin.html" target="_blank">The Alevin Documentation</a>
for detailed usage guidelines.
|
|
|
0.6
|
Alevin 1.5.2 - beta release
|
bhill@broadinstitute.org |
GenePattern production (new)
|
|
|
|
Salmon.Indexer
Salmon (version 1.6.0) transcriptome indexer.<br>
See: <a href="https://salmon.readthedocs.io/en/latest/salmon.html#using-salmon" target="_blank">The Salmon User Guide</a>
for detailed usage guidelines.
|
|
|
0.5
|
Updated to Salmon 1.6.0 and added support for transcriptome only index
|
bhill@broadinstitute.org |
GenePattern production (new)
|
|
|
|
Salmon.Quant
Perform transcript-level quantification of RNA-seq data using Salmon (version 1.6.0).<br>
See: <a href="https://salmon.readthedocs.io/en/latest/salmon.html#using-salmon" target="_blank">The Salmon User Guide</a>
for detailed usage guidelines.
|
|
|
0.9
|
Update to Salmon v1.6.0 and add Gencode Human release v39 and Mouse release vM28- beta update
|
bhill@broadinstitute.org |
GenePattern production (new)
|
|
|
|
sample_combat_results
describe it here
|
|
|
1
|
0
|
ncastano |
Created on server
|
|
|
|
SamTools.FastaIndex
Indexes a reference sequence in the FASTA format
|
|
|
0.3
|
Improved error message for different line length in sequence error
|
tabor |
GenePattern dev
|
|
|
|
ScanpyQC
Create Scanpy Quality Control Plots to enable unblinded dataset filtering with ScanpyUtilities
|
|
|
2
|
first Jenkins prerelease
|
acastanza |
GenePattern production (new)
|
|
|
1
|
first Jenkins prerelease
|
ted |
GenePattern production (new)
|
|
|
|
ScanpyUtilities
Scanpy preprocessing of an h5 single cell RNASeq dataset
|
|
|
1
|
Updated h5ad version and added mitochondrial filtering support on 10/04/2021
|
ted |
GenePattern production (new)
|
|
|
1.3
|
Updated h5ad version and added mitochondrial filtering support on 10/04/2021
|
tabor |
GenePattern dev
|
|
|
0.8
|
Working revision from Gevaert lab git repo on 10/16/18
|
ted |
Installed from zip
|
|
|
0.7
|
Working revision from Gevaert lab git repo on 10/16/18
|
ted |
Installed from zip
|
|
|
0.06
|
Working revision from Gevaert lab git repo on 10/16/18
|
ted |
Installed from zip
|
|
|
0.05
|
Working revision from Gevaert lab git repo on 10/16/18
|
ted |
Installed from zip
|
|
|
0.04
|
Working revision from Gevaert lab git repo on 10/16/18
|
ted |
Installed from zip
|
|
|
0.03
|
Working revision from Gevaert lab git repo on 10/16/18
|
ted |
Installed from zip
|
|
|
0.2
|
Working revision from Gevaert lab git repo on 10/16/18
|
ted |
Installed from zip
|
|
|
0.02
|
Working revision from Gevaert lab git repo on 10/16/18
|
ted |
Installed from zip
|
|
|
|
scVelo
Module for performing basic velocity analysis using the scVelo protocol on ScanpyUtilities processed datasets
|
|
|
2
|
Initial release
|
tabor |
GenePattern production (new)
|
|
|
1
|
Initial release
|
bhill@broadinstitute.org |
GenePattern production (new)
|
|
|
|
sec.clones
describe it here
|
|
|
1
|
0
|
kamyar |
Created on server
|
|
|
|
SelectFeaturesColumns
Takes a 'column slice' from a .res, .gct, .snp, .cn, .loh, .odf, or .cls file.
|
|
|
4
|
Added support for .snp, .cn, and .loh files
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
3
|
Added cls file input option and updated task description
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
SelectFeaturesRows
Generate a .res, .gct, .snp, .cn, .loh, or .odf file containing only specified features (i.e. rows).
|
|
|
4
|
Added support for .snp, .cn, and .loh files
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
SelectFileMatrix
A helper module which selects a matrix out of a delimited text file.
|
|
|
1
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
selectingGenes_329
|
|
|
1
|
|
lydia.lam |
Created on server
|
|
|
|
SelectSNPProbes
Filter to keep just copy number probes
|
|
|
0.4
|
Modified to append extension of input file to output file and input and output file formats and added doc
|
tabor |
GenePattern dev
|
|
|
|
SetFCSKeywords
Sets keyword/value(s) in a Flow Cytometry Standard (FCS) file.
|
|
|
2
|
Fix for parsing empty keyword values
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
seurat
describe it here
|
|
|
2
|
0
|
ted |
Created on server
|
|
|
1
|
0
|
ted |
Created on server
|
|
|
|
Seurat.BuffetPreprocessing
Seurat preprocessing
|
|
|
2
|
display seurat object sizes
|
jonzamora |
Created on server
|
|
|
1
|
Editing parameter groups
|
jonzamora |
Created on server
|
|
|
|
Seurat.Clustering
Companion module for the <a href="https://notebook.genepattern.org/services/sharing/notebooks/376/preview/">Seurat notebook</a>. Performs clustering and marker identification on single cell data.
|
|
|
1.2
|
Updating to run Seurat 4.0.3
|
edjuaro |
GenePattern dev
|
|
|
1.1
|
Updating to run Seurat 4.0.3
|
edjuaro |
GenePattern dev
|
|
|
0.6
|
Adding link to notebeook + patching a parameter so it reflects the actual options.
|
edjuaro |
GenePattern dev
|
|
|
0.5
|
Adding number of cluster markers as option + fixed docker container.
|
edjuaro |
GenePattern dev
|
|
|
0.3
|
Adding number of cluster markers as option.
|
edjuaro |
GenePattern dev
|
|
|
0.2
|
Updating module description.
|
edjuaro |
GenePattern dev
|
|
|
|
Seurat.DietPreprocessing
Seurat Preprocessing
|
|
|
1
|
Include new parameter for Diet Seurat Preprocessing
|
jonzamora |
Created on server
|
|
|
|
Seurat.IntegrateData
Batch Correction for Seurat Objects
|
|
|
1.3
|
Upgrading to Seurat V4 and fixing a bug in the command line and file name
|
edjuaro |
Created on server
|
|
|
|
Seurat.IntegrateData
Batch Correction for Seurat Objects
|
|
|
4.1
|
Upgrading to Seurat V4 and fixing a bug in the command line and file name
|
tabor |
GenePattern dev
|
|
|
|
Seurat.Preprocessing
Seurat preprocessing
|
|
|
4
|
Upgrading to Seurat 4.0.3
|
edjuaro |
GenePattern production (new)
|
|
|
4.1
|
Upgrading to Seurat 4.0.3
|
edjuaro |
GenePattern dev
|
|
|
3
|
Editing parameter groups
|
jonzamora |
Installed from zip
|
|
|
3.2
|
Upgrading to Seurat 4.0.3
|
edjuaro |
GenePattern dev
|
|
|
3.1
|
Upgrading to Seurat 4.0.3
|
edjuaro |
GenePattern dev
|
|
|
1
|
Editing parameter groups
|
edjuaro |
Installed from zip
|
|
|
1.1
|
Upgrading to Seurat v4.0.3
|
edjuaro |
GenePattern dev
|
|
|
0.12
|
Reading the RDS file
|
edjuaro |
GenePattern dev
|
|
|
0.11
|
Reading the RDS file
|
edjuaro |
GenePattern dev
|
|
|
0.10
|
Reading the RDS file
|
edjuaro |
GenePattern dev
|
|
|
0.9
|
Parsing zip files v3
|
edjuaro |
GenePattern dev
|
|
|
|
Seurat.PreprocessingNullFeatures
Seurat preprocessing
|
|
|
1
|
Upgrading to Seurat 4.0.3
|
jonzamora |
Created on server
|
|
|
|
Seurat.QC
Seurat quality control (First step in the Seurat Suite), using Seurat version 4.0.3.
|
|
|
4
|
Reading new version of HCA (Loom)
|
edjuaro |
GenePattern production (new)
|
|
|
4.11
|
Reading new version of HCA (Loom), fixing the url reading bug (added a new parameter)
|
edjuaro |
Installed from zip
|
|
|
3.3
|
Reading new version of HCA (Loom)
|
edjuaro |
GenePattern dev
|
|
|
3.1
|
Making the creation of the TXT file optional.
|
jonzamora |
Installed from zip
|
|
|
2
|
Renaming some parameters
|
edjuaro |
GenePattern production (new)
|
|
|
0.16
|
Renaming some parameters
|
edjuaro |
GenePattern dev
|
|
|
|
Seurat.VisualizeMarkerExpression
Visualize Marker Expression as violin plots and on a UMap. To be used after Seurat.Clustering
|
|
|
2
|
Same as first version, oficial release.
|
edjuaro |
GenePattern production (new)
|
|
|
1
|
First version
|
edjuaro |
GenePattern production (new)
|
|
|
|
seuratclustertestedw
Companion module for the <a href="https://notebook.genepattern.org/services/sharing/notebooks/376/preview/">Seurat notebook</a>. Performs clustering and marker identification on single cell data.
|
|
|
2
|
Updating to run Seurat 4.0.3
|
edwin5588 |
Created on server
|
|
|
1
|
Updating to run Seurat 4.0.3
|
edwin5588 |
Created on server
|
|
|
|
sfs
describe it here
|
|
|
2
|
0
|
liuzaoqu |
Created on server
|
|
|
1
|
0
|
liuzaoqu |
Created on server
|
|
|
|
shRNAscores
Outputs fold change, signal to noise and modified score (which deweights highly variable hps from reference control) for RNAI HP scoring
|
|
|
0.4
|
changed name of module
|
tabor |
GenePattern dev
|
|
|
|
signatures
describe it here
|
|
|
1
|
0
|
tlobo |
Created on server
|
|
|
|
Simple_ssGSEA_and_ROC_curve
|
|
|
1
|
|
TaeHoon5314 |
Created on server
|
|
|
|
skcm.clustering
skcm clustering
|
|
|
3
|
|
eshelden |
Created on server
|
|
|
2
|
|
eshelden |
Created on server
|
|
|
1
|
|
eshelden |
Created on server
|
|
|
|
SKCM2
describe it here
|
|
|
1
|
0
|
rohits |
Created on server
|
|
|
|
SKCMConCluFPKMUQ_12052018
|
|
|
1
|
|
lydia.lam |
Created on server
|
|
|
|
SKCMConsensusCluster_12032018
|
|
|
1
|
|
lydia.lam |
Created on server
|
|
|
|
SKCMConsensusClusterFPKMUQ_12042018
|
|
|
1
|
|
lydia.lam |
Created on server
|
|
|
|
SLE_Data
|
|
|
2
|
|
sc9295 |
Created on server
|
|
|
1
|
|
sc9295 |
Created on server
|
|
|
|
sleep
just take some time and write a file
|
|
|
3
|
|
ted |
Installed from zip
|
|
|
|
snp
describe it here
|
|
|
1
|
0
|
dinayamin |
Created on server
|
|
|
|
SNP.Copy.Number.and.Loss.of.Heterozygosity.Estimation
|
|
|
6
|
|
Niktdak |
Created on server
|
|
|
5
|
|
Niktdak |
Created on server
|
|
|
4
|
|
Niktdak |
Created on server
|
|
|
3
|
|
Niktdak |
Created on server
|
|
|
2
|
|
Niktdak |
Created on server
|
|
|
|
SNPFileCreator
Performs normalization and probe-level summarization to generate a SNP file for a set of Affymetrix SNP chip CEL files.
|
|
|
3.12
|
Modified to output only snp format
|
tabor |
GenePattern dev
|
|
|
1
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
SNPFileCreator_1chip
Processes Affymetrix SNP probe-level data into expression values
|
|
|
0.3
|
|
tabor |
GenePattern dev
|
|
|
|
SNPFileCreator_SNP6
Performs normalization and probe-level summarization to generate a SNP file for a set of Affymetrix SNP chip CEL files.
|
|
|
1.2
|
Updated doc to html
|
tabor |
GenePattern dev
|
|
|
|
SNPFileSorter
Sorts a .snp file by Chromosome and location
|
|
|
1
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
SNPMultipleSampleAnalysis
Determine Regions of Concordant Copy Number Aberrations
|
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1
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
1.3
|
changed cytoband to <libdir>CytoBands.txt - per Josh's suggestion in gpat-189
|
tabor |
GenePattern dev
|
|
|
|
SnpViewer
Displays a heat map of snp data
|
|
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3
|
Fixes bug with legend thresholds
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
SOMClustering
Self-Organizing Maps algorithm
|
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2
|
Updated to latest file parsers and annotated for GP 1.4
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
SOMClusterViewer
Visualize clusters created with the SOM algorithm
|
|
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5
|
Fixes redraw bug
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
5.1
|
Added ability to scroll the left panel
|
pcarr@broadinstitute.org |
GenePattern beta
|
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sortSam
|
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1
|
|
bb3029@cumc.columbia.edu |
Created on server
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SPARCS
|
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1
|
|
sheilazt |
Created on server
|
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|
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SparseHierarchicalClustering
Cluster the samples in a data matrix using an adaptively-chosen subset of the features.
|
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1
|
Public Release
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
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1.1
|
Public Release
|
tabor |
GenePattern dev
|
|
|
|
spatialGE.Preprocessing
The package spatialGE provides a collection of tools for the visualization of gene expression from spatially-resolved transcriptomic experiments. The data input methods have been designed so that any data can be analyzed as long as it contains gene expression counts per region of interest (ROI), spot, or cell, and the spatial coordinates of those ROIs, spots, or cells, as it is generated in platforms such as GeoMx, Visium, and CosMx-SMI. The spatialge.Preprocessing module performs initial data ingestion, filtering, transform and pseudo-bulk operations to prepare data for further processing. Order of operations are: ingestion, filter, pseudobulk, transform.
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|
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5
|
Strip .tar from output filenames if its part of the input filename. Stop putting .rds on the rds file twice.
|
ted |
GenePattern production (new)
|
|
|
4
|
Updated to use GitHub Pages doc url rather than doc.html
|
ted |
GenePattern production (new)
|
|
|
3
|
Updated to use GitHub Pages doc url rather than doc.html
|
ted |
GenePattern production (new)
|
|
|
2
|
Updated to use GitHub Pages doc url rather than doc.html
|
ted |
GenePattern production (new)
|
|
|
|
spatialGE.SpatialAutocorrelation
This function performs spatial statistics analysis on spatial transcriptomics data using the SThet module.
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1
|
|
ted |
GenePattern production (new)
|
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|
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spatialGE.STclust
This function performs spatial clustering on gene expression data using the STclust method.
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1
|
|
edwin5588 |
GenePattern production (new)
|
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|
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spatialGE.STenrich
Detect genes showing spatial expression patterns (e.g., hotspots). Tests if spots/cells with high average expression of a gene set shows evidence of spatial aggregation.
|
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1
|
Initial development release
|
tabor |
GenePattern production (new)
|
|
|
|
SplitColumns
Creates a separate file for each column specified from the input file
|
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1
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
SplitDatasetTrainTest
Splits a dataset (and cls file) into a number of train and test subsets
|
|
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4
|
Added output types train.0.gct, test.0.gct, train.1.gct, test.1.gct, et cetera
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
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ssGESA
|
|
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1
|
|
georgewu |
Created on server
|
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ssGESEA
describe it here
|
|
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1
|
0
|
Kkkkate |
Created on server
|
|
|
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ssgsea
|
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|
1
|
|
christophe.goncalve@mail.mcgill.ca |
Created on server
|
|
|
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ssGSEA
|
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1
|
|
effe_li |
Created on server
|
|
|
|
ssGSEA
Performs single sample GSEA. NOTE: with the release of v10.0.1, this module was renamed from "ssGSEAProjection" to just "ssGSEA"
|
|
|
10.1.0
|
10/03/2022 : Updated to Human MSigDB v2022.1.Hs and Mouse MSigDB 2022.1.Mm.
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
10.0.12
|
09/15/2022 : Updated to Human MSigDB v2022.1.Hs. Direct support for Mouse MSigDB 2022.1.Mm is not yet available
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
10.0.11
|
01/19/2022 : Updated to MSigDB v7.5.1.
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
10.0.10
|
01/12/2022 : Updated to MSigDB v7.5.
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
10.0.9
|
04/22/2021 : Fixed minor typo.
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
10.0.8
|
04/01/2021 : Updated for MSigDB v7.4.
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
10.0.7
|
03/22/2021 : Updated for MSigDB v7.3.
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
10.0.6
|
12/16/2020 : Fix for single sample GCT files and single set GMX files.
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
10.0.4
|
09/23/2020 : Updated to MSigDB v7.2.
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
10.0.3
|
04/02/2020 : Updated to MSigDB v7.1.
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
10.0.2
|
03/10/2020 : Renamed from ssGSEAProjection. Updated to R-3.2. Documentation updates.
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
9.1.2
|
Updated to give access to MSigDB v7.0. Unified the Gene Set DB selector parameters and better downloading of MSigDB files. Removed Java dependency. Updated to give access to MSigDB v7.0. Added a no-normalize option as the default.
|
eby@broadinstitute.org |
GenePattern production (new)
|
|
|
|
ssgsea
describe it here
|
|
|
1
|
0
|
ltinoue |
Created on server
|
|
|
|
ssGSEA.Analysis
describe it here
|
|
|
1
|
0
|
amassa |
Created on server
|
|
|
|
ssGSEA.Eide.dataset
|
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|
2
|
|
hhalse |
Created on server
|
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|
1
|
|
hhalse |
Created on server
|
|
|
|
ssGSEA.ROC
Generate ROC curves and calculate the AUC from ssGSEA results and a binary phenotype classification.
|
|
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1
|
|
ted |
GenePattern production (new)
|
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|
|
ssGSEA.success
describe it here
|
|
|
1
|
0
|
ldzier |
Created on server
|
|
|
|
ssGSEA.to.ConstellationMap
describe it here
|
|
|
1
|
0
|
mverber1114 |
Created on server
|
|
|
|
ssGSEA_1
|
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1
|
|
mestrada |
Created on server
|
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|
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ssGSEA_20_SCLC
ssGSEA for 20 SCLC
|
|
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1
|
|
MarcoMernberger |
Created on server
|
|
|
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ssGSEA_allgenesets
|
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|
5
|
|
samuel1 |
Created on server
|
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|
4
|
|
samuel1 |
Created on server
|
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3
|
|
samuel1 |
Created on server
|
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|
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ssGSEA_and_ROC_for_set_eight
|
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3
|
|
thk1 |
Created on server
|
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2
|
|
thk1 |
Created on server
|
|
|
|
ssGSEA_CCLE_v1
describe it here
|
|
|
1
|
0
|
mitsuishi.y |
Created on server
|
|
|
|
ssGSEA_JT
describe it here
|
|
|
1
|
0
|
sturcan1 |
Created on server
|
|
|
|
ssGSEA_Luca
|
|
|
1
|
|
lucaT |
Created on server
|
|
|
|
ssGSEA_prompt
|
|
|
2
|
|
MarcoMernberger |
Created on server
|
|
|
1
|
|
MarcoMernberger |
Created on server
|
|
|
|
ssGSEA_test
describe it here
|
|
|
1
|
0
|
HauslerD |
Created on server
|
|
|
|
ssgsea_viz_testing
describe it here
|
|
|
1
|
0
|
samuel1 |
Created on server
|
|
|
|
ssGSEAandROC
|
|
|
5
|
|
TaeHoon5314 |
Created on server
|
|
|
4
|
|
TaeHoon5314 |
Created on server
|
|
|
3
|
|
TaeHoon5314 |
Created on server
|
|
|
2
|
|
TaeHoon5314 |
Created on server
|
|
|
1
|
|
TaeHoon5314 |
Created on server
|
|
|
|
ssGSEATest1
|
|
|
1
|
|
anicolau |
Created on server
|
|
|
|
ssgseaviewing
describe it here
|
|
|
1
|
0
|
guest_96395 |
Created on server
|
|
|
|
STAD
describe it here
|
|
|
1
|
0
|
ZANGYue |
Created on server
|
|
|
|
STAR.aligner
STAR (Spliced Transcripts Alignment to a Reference) 2.7.10b is a fast RNA-seq reads to genome mapper. It differs from other mappers as TopHat in that it gains speed at the expense of consuming more RAM and that it incorporates transcriptome annotation at the indexing build stage rather than at the analysis stage. It can optionally detect non-canonical splices and chimeric transcripts.
|
|
|
2
|
Adding support for gzipped input data
|
edwin5588 |
GenePattern production (new)
|
|
|
1.4
|
Update to STAR 2.7.10.b
|
ted |
GenePattern dev
|
|
|
1.3
|
Genome folder stubbed out until it can be hosted somewhere retrievable via http instead of ftp
|
ted |
GenePattern dev
|
|
|
|
star.alignment
describe it here
|
|
|
2
|
0
|
csusm |
Created on server
|
|
|
1
|
0
|
csusm |
Created on server
|
|
|
|
STAR.indexer
The STAR indexer (version 2.7.10b) makes from a series of fastA files containing a genome an index for use with the STAR spliced read to genome aligner. It can optionally (but highly recommended !) incorporate information about known intron-exon junctions.
|
|
|
1
|
Rename index.dir parameter to output.file
|
ted |
GenePattern production (new)
|
|
|
0.50
|
Rename index.dir parameter to output.file
|
ted |
GenePattern dev
|
|
|
0.48
|
Update to STAR 2.7.10b
|
ted |
GenePattern dev
|
|
|
0.46
|
Update to STAR 2.7.1a
|
ted |
GenePattern dev
|
|
|
|
STREAM.DetectDifferentiallyExpressedGenes
Used to detect differentially expressed genes between pairs of branches.
|
|
|
0.12
|
inital revision
|
ted |
Installed from zip
|
|
|
|
STREAM.DetectLeafGenes
Detect marker genes for each leaf branch.
|
|
|
0.12
|
inital revision
|
ted |
Installed from zip
|
|
|
|
STREAM.DetectTransitionGenes
Detects the transition genes for each branch of a STREAM trajectory.
|
|
|
0.3
|
inital revision
|
ted |
Installed from zip
|
|
|
|
STREAM.DimensionReduction
Perform dimension reduction on the dataset to make it easier to reliably assess similarity or distances between cells. Starting from the genes selected in the STREAM.FeatureSelection module, we project cells to a lower dimensional space using a non-linear dimensionality reduction method.
|
|
|
0.7
|
inital revision
|
tabor |
GenePattern dev
|
|
|
0.6
|
inital revision
|
ted |
Installed from zip
|
|
|
0.5
|
inital revision
|
ted |
Installed from zip
|
|
|
|
STREAM.ElasticPrincipalGraph
STREAM (Single-cell Trajectories Reconstruction, Exploration And Mapping) is an interactive pipeline capable of disentangling and visualizing complex branching trajectories from both single-cell transcriptomic and epigenomic data. STREAM.ElasticPrincipalGraph is uses elastic principal graph learning to calculate a pseudotime trajectory.
|
|
|
0.4
|
inital revision
|
ted |
Installed from zip
|
|
|
|
STREAM.EPGAdjustFinalGraph
Adjust the final EPG trajectory structure by pruning, extending and otherwise modifying the branches to optimize for single-cell data
|
|
|
0.6
|
inital revision
|
ted |
Installed from zip
|
|
|
|
STREAM.FeatureSelection
Select either or both of the most variable genes and then find the principal components using PCA. These will then be available for the downstram trajectory analysis.
|
|
|
0.6
|
inital revision
|
ted |
Installed from zip
|
|
|
|
STREAM.Plot2DVisualization
STREAM.Plot2DVisualization is used to check if there is clear meaningful trajectory pattern via TSNE or UMAP 2-D plots. If so, we can continue the STREAM analysis; If not, go back to previous steps (preprocessing, feature selection and dimension reduction) to modify the parameters.
|
|
|
0.15
|
inital revision
|
ted |
Installed from zip
|
|
|
0.14
|
inital revision
|
ted |
Installed from zip
|
|
|
|
STREAM.Preprocess
Preprocess single cell RNA-seq data to prepare it for the STREAM trajectory analysis. This module will normalize, log transform, filter and remove mitochondiral genes.
|
|
|
0.4
|
inital revision
|
ted |
Installed from zip
|
|
|
|
STREAM.SeedEPGStructure
Seeding the initial elastic principal graph prior to starting the trajectory learning process.
|
|
|
0.4
|
inital revision
|
ted |
Installed from zip
|
|
|
|
STREAM.VisualizeTrajectories
Generates flat tree subway and stream plots that intuitively represents trajectories as linear segments on a 2D plane
|
|
|
0.16
|
inital revision
|
ted |
Installed from zip
|
|
|
|
SUBMAP
describe it here
|
|
|
1
|
0
|
D201981538 |
Created on server
|
|
|
|
SubMap
Maps subclasses between two data sets
|
|
|
4
|
Changed default value for the p-value correction method parameter and fixed bug which occurs when there is one instance of a class
|
ted |
GenePattern production (new)
|
|
|
3
|
Changed default value for the p-value correction method parameter and fixed bug which occurs when there is one instance of a class
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
SurvivalCurve
Draws a survival curve based on a cls file
|
|
|
3
|
Modified to use R 2.7 and Cairo to output images in PNG format
|
ted |
Installed from zip
|
|
|
2
|
added pdf survival curve output format
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
SurvivalDifference
Tests for survival difference based on cls file
|
|
|
1
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
SVM
Classify samples using SVM
|
|
|
4
|
Compute confidence for prediction results.
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
4.1
|
Added check that the user provided saved model is an SVM model
|
tabor |
GenePattern dev
|
|
|
|
SysBio_HW1
|
|
|
5
|
|
ps1277 |
Created on server
|
|
|
4
|
|
ps1277 |
Created on server
|
|
|
|
T.cell.volcano.test
|
|
|
1
|
|
carmenyong |
Created on server
|
|
|
|
Tangram
A method for spatial alignment of single cell transcriptomic data. See <a href=https://github.com/genepattern/Tangram/blob/main/README.md>documentation</a> for details on use cases.
|
|
|
5
|
Docker image update to v1.0
|
edwin5588 |
GenePattern production (new)
|
|
|
|
TCGA.LIHC.beta.cat
describe it here
|
|
|
1
|
0
|
fahmida.rasha@utsouthwestern.edu |
Created on server
|
|
|
|
TCGA.LIHC.CTNNB1.step1
describe it here
|
|
|
2
|
0
|
fahmida.rasha@utsouthwestern.edu |
Created on server
|
|
|
1
|
0
|
fahmida.rasha@utsouthwestern.edu |
Created on server
|
|
|
|
TCGA.SampleSelection
Retrieve TCGA data from Broad FireBrowse and perform sample selection on the basis of expression levels for specific genes of interest for analysis using GSEA tools.
|
|
|
3
|
Update for non-float MSigDB version numbers
|
ted |
Installed from zip
|
|
|
2
|
Update for non-float MSigDB version numbers
|
edwin5588 |
GenePattern production (new)
|
|
|
1
|
Update for non-float MSigDB version numbers
|
edwin5588 |
GenePattern production (new)
|
|
|
0.14
|
Update for non-float MSigDB version numbers
|
bhill@broadinstitute.org |
GenePattern production (new)
|
|
|
|
TCGA.ssGSEA.ROC
Pipeline for ssGSEA_ROC analysis of TCGA samples
|
|
|
10
|
|
acastanza |
Created on server
|
|
|
9
|
|
acastanza |
Created on server
|
|
|
8
|
|
acastanza |
Created on server
|
|
|
7
|
|
acastanza |
Created on server
|
|
|
6
|
|
acastanza |
Created on server
|
|
|
5
|
|
acastanza |
Created on server
|
|
|
|
TCGA.to.DESeq2
Retrieve count data from TCGA and run DESeq2 on it, also outputting normalized counts for GSEA and other tools
|
|
|
1
|
|
acastanza |
Created on server
|
|
|
|
TCGA_BRCA
describe it here
|
|
|
1
|
0
|
l.chavez |
Created on server
|
|
|
|
TCGA_THCA
|
|
|
1
|
|
haiyan |
Created on server
|
|
|
|
TCGABRCA
describe it here
|
|
|
1
|
0
|
Jasminetee |
Created on server
|
|
|
|
TCGACNV
|
|
|
1
|
|
zhouguowei |
Created on server
|
|
|
|
TCGAImporter
This module imports data from TCGA by taking in a GDC manifest file, downloading the files listed on that manifest, renaming them to be human-friendly, and compiling them into a GCT file to be computer-friendly.
|
|
|
6
|
Adding metadata to the docker container & updating to version 1.5 of the CLI.
|
edjuaro |
GenePattern production (new)
|
|
|
5
|
Updating module to use the new docker container.
|
edjuaro |
GenePattern production (new)
|
|
|
5.2
|
Bugfix: duplicated gene after translation. Also using new format in the command line on the manifest file.
|
edjuaro |
https://modulerepository.genepattern.org/gpModuleRepository//?env=dev
|
|
|
|
TCGAImporter_test_pipelne
Download and collapse small dataset
|
|
|
3
|
1.0
|
edjuaro |
Installed from zip
|
|
|
|
TedsAttackTest
A module for testing attacks against our server
|
|
|
999999999
|
|
ted |
Installed from zip
|
|
|
|
test
describe it here
|
|
|
2
|
0
|
Della_123 |
Created on server
|
|
|
1
|
0
|
Della_123 |
Created on server
|
|
|
|
test
describe it here
|
|
|
1
|
0
|
guest_97887 |
Created on server
|
|
|
|
Test.
|
|
|
1
|
|
Devansh |
Created on server
|
|
|
|
test2
describe it here
|
|
|
1
|
0
|
Della_123 |
Created on server
|
|
|
|
test3
describe it here
|
|
|
2
|
0
|
ted |
Created on server
|
|
|
1
|
0
|
ted |
Created on server
|
|
|
|
tfsites.FindTfSitesAlteredBySequenceVariation
FindTfSitesAlteredBySequenceVariation reports the effects of all possible in silico single-nucleotide variants (SNVs) in a given sequence, for one transcription factor. Possible SNV effects include increasing (or optimizing) the affinity/score of a binding site, decreasing the affinity/score of a binding site, deleting a binding site, or creating a binding site.
|
|
|
1
|
Draft initial release
|
ted |
GenePattern production (new)
|
|
|
|
tfsites.GenerateMotifDatabase
GenerateMotifDatabase can be used to obtain position weight matrix (PWM) data to score binding sites in other TFSites modules. This tool extracts the PFM(s) for one or more transcription factor(s) of interest and then converts each PFM to its respective PWM.
|
|
|
1
|
Draft initial release
|
ted |
GenePattern production (new)
|
|
|
|
tfsites.NormalizeTfDNAAffinityData
NormalizeTfDnaAffinityData generates a relative affinity dataset which can then be used in other TFSites modules to score binding sites. This tool normalizes a raw affinity dataset relative to the sequence with the highest value that follows the core binding site definition. The resulting dataset will report the relative affinity value for every sequence in the original dataset, ranging from 0 to 1.
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1
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Draft initial release
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ted |
GenePattern production (new)
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tfsites.VisualizeTFSitesOnSequences
Annotates transcription factor binding sites across a DNA sequence. Multiple transcription factors can be analyzed. Each binding site is labeled with a unique binding site ID and its start and end position. If reference data is provided for a transcription factor, the affinity/score of this site will be labeled and the intensity of the binding site's color will be proporti
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1
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Draft initial release
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ted |
GenePattern production (new)
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TLS.signiture
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1
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sholmes.vs.jmoriarty@gmail.com |
Created on server
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TmapToGct
Converts a TMAP file to GCT format
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1
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pcarr@broadinstitute.org |
GenePattern production (new)
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tmp
describe it here
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1
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0
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JieLan |
Created on server
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tracking.to.GCT
Seurat preprocessing
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1
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Parsing zip files
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marjanbrz |
Installed from zip
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Transcriptomics.Analysis
describe it here
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1
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0
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cherkaos |
Created on server
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TransposeDataset
Transpose a Dataset - .res .gct, .odf
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3
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Added gct as an output format
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pcarr@broadinstitute.org |
GenePattern production (new)
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Trial
describe it here
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1
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0
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ratna.wijaya |
Created on server
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Trial1
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1
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RebeccaAstley |
Created on server
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Trimmomatic
Provides a variety of options for trimming Illumina FASTQ files of adapter sequences and low-quality reads.
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2
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Replaced gpftp with datasets
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tabor |
GenePattern production (new)
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1.4
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updated convert phred scores value to preserve no convert option in pipelines
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pcarr@broadinstitute.org |
GenePattern production (new)
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tryout
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1
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Himmel |
Created on server
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TSGH.PM2.5.pathway.analysis
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1
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kunghsiuni |
Created on server
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tst
tst
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2
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edwin5588 |
Created on server
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1
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edwin5588 |
Created on server
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Tutorial
describe it here
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3
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lalevesque95 |
Created on server
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2
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0
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lalevesque95 |
Created on server
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1
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0
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lalevesque95 |
Created on server
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tutorial.1
describe it here
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3
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0
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Hoyaka |
Created on server
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2
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0
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Hoyaka |
Created on server
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1
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0
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Hoyaka |
Created on server
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Tutorial.Pipeline
Generation of heat map of the expressed gene
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2
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0
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Hoyaka |
Created on server
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1
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0
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Hoyaka |
Created on server
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tutorial01
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1
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renyow |
Created on server
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Tutorial_creating_a_workflow
describe it here
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1
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0
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beaver9701 |
Created on server
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tximport.DESeq2
Imports RNA-seq quantifications from frequently used pipelines using the tximport package and outputs a DESeq2 "normalized counts" file in .GCT format suitable for use with GSEA, and/or a TPM .GCT suitable for ssGSEA.<br>
If a Sample Info file is provided containing assignments of samples to phenotypes, gene level differential expression will be calculated using DESeq2 for the two phenotypes.
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5
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edwin5588 |
GenePattern production (new)
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4
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acastanza |
GenePattern production (new)
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3.8
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ted |
GenePattern dev
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3.5
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ted |
GenePattern dev
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txt2odf
This module turns a TXT file into an ODF file which can be used with other GenePattern Modules.
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3
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Cleaning up the release
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edjuaro |
GenePattern production (new)
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2
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First production release
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edjuaro |
GenePattern production (new)
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txt2odf.20211130.colparams
This module turns a TXT file into an ODF file which can be used with other GenePattern Modules.THIS MODULE IS FOR USE IN THE Dec 21, 2021 workshop and is in active development
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1.3
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Making module public for workshop
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tabor |
GenePattern dev
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UBE2D3TCGA.HCC
describe it here
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1
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0
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HN |
Created on server
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UCEC
describe it here
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1
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0
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Team_Julia |
Created on server
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UniquifyLabels
Makes row and column labels unique
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1
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pcarr@broadinstitute.org |
GenePattern production (new)
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UntitledPipeline1556
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1
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YWW |
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guest_96467 |
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liuhao |
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liuhao |
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Jianfeng |
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lisafleischer1 |
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Devansh |
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inga-maria.launonen@helsinki.fi |
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LilHasegawa |
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Mattia_gp2 |
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caitlyn3@stanford.edu |
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wangyu |
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wangyu |
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wangyu |
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wangyu |
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hhyunji1027@naver.com |
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wangyu |
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hhyunji1027@naver.com |
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hhyunji1027@naver.com |
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YubinXie |
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YubinXie |
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LamantiaMaria@gmail.com |
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studyong |
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liuhao |
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hgx_sherry@163.com |
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ACC expression
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tunde.golenar@mail.mcgill.ca |
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s.aishwaryabiotech@gmail.com |
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wangyu |
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sholmes.vs.jmoriarty@gmail.com |
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vlkjvlkj |
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mbird |
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vinodyadav2083@gmail.com |
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wangyu |
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alberto.peloso2 |
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Monika Lewinska |
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lamantiamaria@gmail.com |
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s
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1.0
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ryy |
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seisen27 |
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TaeHoon2042 |
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liuyang_fudan |
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qedos |
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liuhao |
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torch2sky |
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greecebry |
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liuhao |
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thk1 |
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liujian |
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Carlin54 |
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ymq |
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liuhao |
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kdkorthauer |
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kdkorthauer |
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kdkorthauer |
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kdkorthauer |
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areum.han98 |
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parkhc2 |
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erietta |
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ktlee201 |
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alberto.peloso |
Created on server
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UntitledPipeline9847
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1
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mats91 |
Created on server
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1
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liuhao |
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Kevin.Geistlich |
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Silvia Sabina |
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1
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cmills2@fredhutch.org |
Created on server
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1
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liuhao |
Created on server
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buyangaaa |
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YWW |
Created on server
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|
UploadFile
A utility for users to upload and share a common input file for use by modules within a pipeline.
|
|
|
0.1
|
|
tabor |
GenePattern dev
|
|
|
|
v1
describe it here
|
|
|
1
|
0
|
chanpulin |
Created on server
|
|
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|
Vaccinia.Affymetrix.Analysis.2020
|
|
|
7
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jyothsnagirish |
Created on server
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6
|
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jyothsnagirish |
Created on server
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5
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jyothsnagirish |
Created on server
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4
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jyothsnagirish |
Created on server
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3
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jyothsnagirish |
Created on server
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2
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jyothsnagirish |
Created on server
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1
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jyothsnagirish |
Created on server
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|
Vaccinia.Affymetrix.Analysis.2020.v2
|
|
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2
|
|
jyothsnagirish |
Created on server
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|
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1
|
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jyothsnagirish |
Created on server
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|
|
|
VennDiagram
Displays a Venn diagram
|
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|
1
|
|
pcarr@broadinstitute.org |
GenePattern production (new)
|
|
|
|
view
describe it here
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1
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0
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nicolaco |
Created on server
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viewer
describe it here
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1
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0
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elenapip |
Created on server
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Visualizing.Filtered.DEGs
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2
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alow |
Created on server
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1
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alow |
Created on server
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1.2
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alow |
Created on server
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1.1
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alow |
Created on server
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viz
describe it here
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1
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0
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sophiespo |
Created on server
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Voom.normalise.raw.counts.28921
describe it here
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1
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0
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liana.gynn |
Created on server
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VoomNormalize
Preprocess RNA-Seq count data in a GCT file so that it is suitable for use in GenePattern analyses. Formerly called "PreprocessReadCounts"
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1.2
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Creating anti-logged normalized values as one of the outputs & fixing documentation
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tabor |
GenePattern dev
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0.9
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Rename PreprocessReadCounts to VoomNormalize -- adding this to the description
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edjuaro |
GenePattern production (new)
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0.8
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Rename PreprocessReadCounts to VoomNormalize
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edjuaro |
https://modulerepository.genepattern.org/gpModuleRepository//?env=dev
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0.7
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set 'job.docker.image=genepattern/preprocessreadcounts'; containerize R packages
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pcarr@broadinstitute.org |
https://modulerepository.genepattern.org/gpModuleRepository//?env=dev
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0.6
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pcarr@broadinstitute.org |
GenePattern beta
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WeightedVoting
Weighted Voting classification
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3
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Added additional feature selection options
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pcarr@broadinstitute.org |
GenePattern production (new)
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1
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Added java flag to allow this to run on unix servers lacking an X display
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pcarr@broadinstitute.org |
GenePattern production (new)
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WeightedVotingXValidation
Weighted Voting classification with Leave-One-Out Cross-Validation
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3
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Added additional feature selection options
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pcarr@broadinstitute.org |
GenePattern production (new)
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2
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Correct ordering of class outputs, output class names in feature files, annotated for GP 1.4, updated file support libraries.
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pcarr@broadinstitute.org |
GenePattern production (new)
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Whole.exome.seq
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1
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1
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silambarasan |
Created on server
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WMr
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1
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wmr23 |
Created on server
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WT_PD1
describe it here
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2
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0
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ssarkar |
Created on server
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1
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0
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ssarkar |
Created on server
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wwy
describe it here
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1
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0
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WWY |
Created on server
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XChromosomeCorrect
Corrects X Chromosome SNP's for male samples.
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3
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pcarr@broadinstitute.org |
GenePattern production (new)
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3.1
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Fixed bug that required sample info file to have a Ploidy(numeric) column
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tabor |
GenePattern dev
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ZipFiles
Zips files
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0.1
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tabor |
GenePattern dev
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